IRI:
http://purl.obolibrary.org/obo/so.owl
Version IRI:
http://purl.obolibrary.org/obo/so/2021-07-12/so.owl
Other visualisation:
Ontology source

Table of Content

  1. Classes
  2. Object Properties
  3. Annotation Properties
  4. Namespace Declarations

Classes

2A_self_cleaving_peptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002224

Added by Dave Sant on October 21, 2019 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/475
has super-classes
polypeptide_regionc

2KB_downstream_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002083

has super-classes
downstream_gene_variantc

2KB_upstream_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001636

has super-classes
upstream_gene_variantc

3_prime_UTR_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002016

has super-classes
3_prime_UTR_variantc

3_prime_UTR_exon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002089

Requested by visze github tracker ID 346.
has super-classes
3_prime_UTR_variantc

3_prime_UTR_intron_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002090

Requested by visze github tracker ID 346.
has super-classes
3_prime_UTR_variantc
coding_transcript_intron_variantc

3_prime_UTR_truncationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002015

has super-classes
3_prime_UTR_variantc

3_prime_UTR_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001624

EBI term 3prime UTR variations - In 3prime UTR.
has super-classes
UTR_variantc
has sub-classes
3_prime_UTR_elongationc, 3_prime_UTR_exon_variantc, 3_prime_UTR_intron_variantc, 3_prime_UTR_truncationc

3D_polypeptide_structure_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001599

has super-classes
translational_product_function_variantc
has sub-classes
complex_3D_structural_variantc, conformational_change_variantc, structural_interaction_variantc

4_methylcytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001919

has super-classes
methylated_cytosinec

500B_downstream_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001634

has super-classes
downstream_gene_variantc

5_carboxylcytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001966

has super-classes
modified_cytosinec

5_formylcytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001961

has super-classes
modified_cytosinec

5_hydroxymethylcytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001960

has super-classes
methylated_cytosinec

5_methylcytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001918

has super-classes
methylated_cytosinec

5_prime_UTR_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002014

has super-classes
5_prime_UTR_variantc

5_prime_UTR_exon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002092

Requested by visze github tracker ID 346.
has super-classes
5_prime_UTR_variantc

5_prime_UTR_intron_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002091

Requested by visze github tracker ID 346.
has super-classes
5_prime_UTR_variantc
coding_transcript_intron_variantc

5_prime_UTR_premature_start_codon_gain_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001988

has super-classes
5_prime_UTR_premature_start_codon_variantc

5_prime_UTR_premature_start_codon_loss_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001989

has super-classes
5_prime_UTR_premature_start_codon_variantc

5_prime_UTR_premature_start_codon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001983

Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
has super-classes
5_prime_UTR_variantc
has sub-classes
5_prime_UTR_premature_start_codon_gain_variantc, 5_prime_UTR_premature_start_codon_loss_variantc, five_prime_UTR_premature_start_codon_location_variantc

5_prime_UTR_truncationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002013

has super-classes
5_prime_UTR_variantc

5_prime_UTR_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001623

EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
has super-classes
UTR_variantc
has sub-classes
5_prime_UTR_elongationc, 5_prime_UTR_exon_variantc, 5_prime_UTR_intron_variantc, 5_prime_UTR_premature_start_codon_variantc, 5_prime_UTR_truncationc

5KB_downstream_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001633

EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
has super-classes
downstream_gene_variantc

5KB_upstream_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001635

EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
has super-classes
upstream_gene_variantc

5S_SINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002276

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
SINE_elementc

7SL_SINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002275

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
SINE_elementc

8_oxoadeninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001967

has super-classes
modified_adeninec

8_oxoguaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001965

has super-classes
modified_guaninec

<new term>c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002117

A_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000619

Binds TFIIIC.
has super-classes
core_eukaryotic_promoter_elementc
has sub-classes
A_box_type_1c, A_box_type_2c

A_box_type_1c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001675

The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
has super-classes
A_boxc
part_ofop some RNApol_III_promoter_type_1c

A_box_type_2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001676

The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
has super-classes
A_boxc
part_ofop some RNApol_III_promoter_type_2c

A_minor_RNA_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000022

has super-classes
RNA_motifc

A_to_C_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000024

has super-classes
purine_to_pyrimidine_transversionc

A_to_G_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000015

has super-classes
purine_transitionc

A_to_T_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000025

has super-classes
purine_to_pyrimidine_transversionc

AACCCT_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001901

has super-classes
core_eukaryotic_promoter_elementc

aberrant_processed_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000681

has super-classes
transcriptc

absent_gene_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002317

Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
has super-classes
null_mutationc
decreased_gene_product_levelc

accessible_DNA_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002331

Added as part of GREEKC terms. See GitHub Issues #531 & #534.
has super-classes
biological_regionc
overlapsop some epigenetically_modified_regionc
has sub-classes
nuclease_hypersensitive_sitec

Ace2_UASc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001857

has super-classes
promoter_elementc

active_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001064

Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
has super-classes
mature_protein_regionc

adaptive_islandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000775

The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
has super-classes
genomic_islandc

AFLP_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001830

Requested by Bayer Cropscience June, 2011.
has super-classes
PCR_productc

alaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001435

A place holder for a cross product with chebi.
has super-classes
amino_acidc

alanine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000211

has super-classes
tRNA_primary_transcriptc

alanyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000254

has super-classes
tRNAc
derives_fromop some alanine_tRNA_primary_transcriptc

allelec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001023

has super-classes
variant_collectionc
variant_ofop some genec
has sub-classes
polymorphic_sequence_variantc

allelic_frequencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002119

Requested by HL7 clinical genomics group.
has super-classes
variant_frequencyc

allelic_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002189

has super-classes
unitary_pseudogenec

allelic_pseudogenic_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002196

has super-classes
pseudogenic_rRNAc

allelic_pseudogenic_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002200

has super-classes
pseudogenic_tRNAc

allelically_excludedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000137

Examples are x-inactivation and immunoglobulin formation.
has super-classes
epigenetically_modifiedc

allelically_excluded_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000897

is equivalent to
epigenetically_modified_genec and (has_qualityop some allelically_excludedc)
has super-classes
epigenetically_modified_genec
has_qualityop some allelically_excludedc

allopolyploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001256

has super-classes
polyploidc

alpha_beta_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100008

has super-classes
polypeptide_secondary_structurec

alpha_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001117

Range.
has super-classes
right_handed_peptide_helixc

alteration_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001508

has super-classes
feature_attributec
has sub-classes
chromosomal_variation_attributec, duplication_attributec, insertion_attributec, inversion_attributec, translocaton_attributec

altered_gene_product_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002314

Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
has super-classes
functional_effect_variantc
has sub-classes
decreased_gene_product_levelc, increased_gene_product_levelc

altered_gene_product_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002318

Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
has super-classes
functional_effect_variantc

alternate_sequence_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001149

Discrete.
has super-classes
polypeptide_variation_sitec

alternately_spliced_gene_encodeing_one_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000503

alternately_spliced_gene_encoding_greater_than_one_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000543

alternatively_splicedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000877

has super-classes
transcript_attributec

alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlappingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001194

alternatively_spliced_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001187

is equivalent to
transcriptc and (has_qualityop some alternatively_splicedc)
has super-classes
transcriptc
has_qualityop some alternatively_splicedc

alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlappingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001244

Alu_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002070

has super-classes
mobile_element_deletionc

Alu_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002063

has super-classes
mobile_element_insertionc

amber_stop_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002333

Added as per GitHub request #537.
has super-classes
stop_codonc

ambisense_ssRNA_viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001202

has super-classes
ss_RNA_viral_sequencec

amino_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001237

Probably in the future this will cross reference to Chebi.
has super-classes
biological_regionc
part_ofop some polypeptidec
has sub-classes
alaninec, argininec, asparaginec, aspartic_acidc, catalytic_residuec, cysteinec, glutamic_acidc, glutaminec, glycinec, histidinec, isoleucinec, leucinec, lysinec, methioninec, modified_amino_acid_featurec, phenylalaninec, prolinec, pyrrolysinec, selenocysteinec, serinec, threoninec, tryptophanc, tyrosinec, valinec

amino_acid_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001604

has super-classes
polypeptide_sequence_variantc

amino_acid_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001605

has super-classes
polypeptide_sequence_variantc

amino_acid_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001606

has super-classes
polypeptide_sequence_variantc
has sub-classes
conservative_amino_acid_substitutionc, non_conservative_amino_acid_substitutionc

amplification_originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000750

has super-classes
origin_of_replicationc

anchor_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000977

Part of an edited transcript only.
has super-classes
transcript_regionc

anchor_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000931

has super-classes
guide_RNA_regionc

androgen_response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001853

has super-classes
DNA_motifc

aneuploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000054

has super-classes
chromosome_number_variationc
has sub-classes
hyperploidc, hypoploidc

aneuploid_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000550

Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
has super-classes
chromosome_structure_variationc
has sub-classes
inversion_derived_aneuploid_chromosomec

annotation_directed_improved_draftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001489

has super-classes
whole_genome_sequence_statusc

anti_ARRETc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001926

Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
has super-classes
telomeric_transcriptc

anticodonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001174

has super-classes
tRNA_regionc
part_ofop some anticodon_loopc

anticodon_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001173

has super-classes
tRNA_regionc

antiparallel_beta_strandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001112

Range.
has super-classes
beta_strandc

antisensec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000077

has super-classes
overlappingc

antisense_lncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001904

Relationship is_a SO:0000644 antisense_RNA added 23 April 2021. See GitHub Issue #443
has super-classes
antisense_RNAc
lncRNAc

antisense_lncRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002182

has super-classes
lncRNA_genec

antisense_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000645

has super-classes
primary_transcriptc

antisense_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000644

has super-classes
ncRNAc
derives_fromop some antisense_primary_transcriptc
has sub-classes
MicF_RNAc, antisense_lncRNAc

AP_1_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001842

has super-classes
promoter_elementc

apicoplast_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001259

is equivalent to
chromosomec and (has_originop some apicoplast_sequencec)
has super-classes
chromosomec
has_originop some apicoplast_sequencec

apicoplast_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000091

is equivalent to
plastid_genec and (has_originop some apicoplast_sequencec)
has super-classes
plastid_genec
has_originop some apicoplast_sequencec

apicoplast_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000743

has super-classes
plastid_sequencec

aptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000031

has super-classes
oligoc
has sub-classes
DNA_aptamerc, RNA_aptamerc

archaeal_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001271

Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
has super-classes
endonuclease_spliced_intronc

archaeosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001323

has super-classes
seven_deazaguanosinec

argininec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001451

A place holder for a cross product with chebi.
has super-classes
amino_acidc

arginine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000212

has super-classes
tRNA_primary_transcriptc

arginyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001036

has super-classes
tRNAc
derives_fromop some arginine_tRNA_primary_transcriptc

ARIAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001925

Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
has super-classes
telomeric_transcriptc

ARRETc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001924

Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
has super-classes
telomeric_transcriptc

ARSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000436

has super-classes
origin_of_replicationc

ARS_consensus_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002004

has super-classes
DNA_motifc
part_ofop some ARSc

asparaginec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001449

A place holder for a cross product with chebi.
has super-classes
amino_acidc

asparagine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000213

has super-classes
tRNA_primary_transcriptc

asparaginyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000256

has super-classes
tRNAc
derives_fromop some asparagine_tRNA_primary_transcriptc

aspartic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001453

A place holder for a cross product with chebi.
has super-classes
amino_acidc

aspartic_acid_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000214

has super-classes
tRNA_primary_transcriptc

aspartyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000257

has super-classes
tRNAc
derives_fromop some aspartic_acid_tRNA_primary_transcriptc

ASPE_primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001698

has super-classes
primerc

assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001248

has super-classes
experimental_featurec
has sub-classes
fragment_assemblyc, sequence_assemblyc

assembly_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000143

has super-classes
experimental_featurec
has sub-classes
contigc, gapc, golden_path_fragmentc, paired_end_fragmentc, readc, restriction_fragmentc, sonicate_fragmentc, tiling_path_fragmentc

assembly_error_correctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001525

has super-classes
sequence_differencec

assortment_derived_aneuploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000058

assortment_derived_aneuploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000803

has super-classes
assortment_derived_variationc

assortment_derived_deficiencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000052

assortment_derived_deficiencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000802

has super-classes
assortment_derived_variationc

assortment_derived_deficiency_plus_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000554

assortment_derived_deficiency_plus_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000801

has super-classes
assortment_derived_variationc

assortment_derived_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000437

assortment_derived_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000800

has super-classes
assortment_derived_variationc

assortment_derived_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001504

has super-classes
chromosome_variationc
has sub-classes
assortment_derived_aneuploidc, assortment_derived_deficiencyc, assortment_derived_deficiency_plus_duplicationc, assortment_derived_duplicationc

asx_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001106

has super-classes
polypeptide_secondary_structurec

asx_turnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000912

has super-classes
polypeptide_turn_motifc
has sub-classes
asx_turn_left_handed_type_onec, asx_turn_left_handed_type_twoc, asx_turn_right_handed_type_onec, asx_turn_right_handed_type_twoc

asx_turn_left_handed_type_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001129

has super-classes
asx_turnc

asx_turn_left_handed_type_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001130

has super-classes
asx_turnc

asx_turn_right_handed_type_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001132

has super-classes
asx_turnc

asx_turn_right_handed_type_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001131

has super-classes
asx_turnc

asymmetric_RNA_internal_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000021

has super-classes
RNA_internal_loopc
has sub-classes
K_turn_RNA_motifc, sarcin_like_RNA_motifc

attB_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000943

has super-classes
integration_excision_sitec

attC_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000950

has super-classes
integration_excision_sitec
part_ofop some integronc

attCtn_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001043

has super-classes
integration_excision_sitec
part_ofop some conjugative_transposonc

attenuatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000140

has super-classes
translation_regulatory_regionc
part_ofop some mRNAc

attI_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000367

has super-classes
integration_excision_sitec
part_ofop some integronc

attL_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000944

has super-classes
integration_excision_sitec

attP_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000942

has super-classes
integration_excision_sitec
part_ofop some phage_sequencec

attR_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000945

has super-classes
integration_excision_sitec

AU_rich_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001180

has super-classes
UTR_regionc
part_ofop some three_prime_UTRc

AUG_initiated_uORFc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002150

has super-classes
uORFc

autocatalytically_spliced_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000588

is equivalent to
intronc and (has_qualityop some ribozymicc)
has super-classes
intronc
has_qualityop some ribozymicc
has sub-classes
group_III_intronc, group_II_intronc, group_I_intronc

autopolyploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001255

has super-classes
polyploidc

autoregulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000471

has super-classes
transcriptionally_regulatedc
has sub-classes
negatively_autoregulatedc, positively_autoregulatedc

autosynaptic_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000136

has super-classes
chromosome_structure_variationc
has sub-classes
dextrosynaptic_chromosomec, laevosynaptic_chromosomec

b s 00003c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00003

b s 0000338c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_0000338

b s 0000339c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_0000339

b s 0000340c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_0000340

b s 0000341c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_0000341

b s 00012c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00012

b s 00026c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00026

b s 00027c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00027

b s 00028c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00028

b s 00029c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00029

b s 00032c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00032

b s 00033c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00033

b s 00036c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00036

b s 00040c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00040

b s 00041c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00041

b s 00042c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00042

b s 00052c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00052

b s 00055c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00055

b s 00063c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00063

b s 00067c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00067

b s 00068c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00068

b s 00069c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00069

b s 00070c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00070

b s 00071c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00071

b s 00072c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00072

b s 00073c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00073

b s 00076c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00076

b s 00077c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00077

b s 00124c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00124

b s 00125c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00125

b s 00128c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00128

b s 00129c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00129

b s 00131c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00131

b s 00134c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00134

b s 00136c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00136

b s 00137c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00137

b s 00140c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00140

b s 00141c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00141

b s 00142c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00142

b s 00143c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00143

b s 00144c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00144

b s 00145c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00145

b s 00146c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00146

b s 00147c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00147

b s 00148c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00148

b s 00149c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00149

b s 00151c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00151

b s 00152c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00152

b s 00153c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00153

b s 00154c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00154

b s 00155c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00155

b s 00156c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00156

b s 00157c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00157

b s 00158c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00158

b s 00159c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00159

b s 00178c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00178

b s 00181c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00181

b s 00182c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00182

b s 00185c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00185

b s 00186c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00186

b s 00187c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00187

b s 00202c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00202

b s 00203c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00203

b s 00204c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00204

b s 00205c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00205

b s 00206c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00206

b s 00207c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00207

b s 00208c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00208

b s 00209c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00209

b s 00210c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00210

b s 00211c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00211

b s 00212c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00212

b s 00213c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00213

b s 00214c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00214

b s 00215c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00215

b s 00216c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00216

b s 00219c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00219

b s 00220c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00220

b s 00221c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00221

b s 00222c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00222

b s 00223c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00223

b s 00224c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00224

b s 00225c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00225

b s 00226c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00226

b s 00227c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00227

b s 00228c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00228

b s 00229c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00229

b s 00230c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00230

b s 00231c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00231

b s 00232c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00232

b s 00233c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00233

b s 00234c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00234

b s 00235c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00235

b s 00246c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00246

b s 00331c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00331

b s 00336c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00336

b s 00337c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BS_00337

B_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000620

Binds TFIIIC.
has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_III_promoter_type_2c

BACc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000153

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
vector_repliconc

BAC_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000764

BAC_cloned_genomic_insertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000992

Requested by Andy Schroder - Flybase Harvard, Nov 2006.
is equivalent to
cloned_genomic_insertc and (derives_fromop some BACc)
has super-classes
cloned_genomic_insertc
derives_fromop some BACc

BAC_endc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000999

Requested by Keith Boroevich December, 2006.
has super-classes
readc
part_ofop some BACc

BAC_read_contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001866

Requested by Bayer Cropscience December, 2011.
is equivalent to
contigc and (has_originop some BACc)
has super-classes
contigc
has_originop some BACc
part_ofop some BACc

bacterial_RNApol_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000613

former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.
has super-classes
prokaryotic_promoterc
has sub-classes
bacterial_RNApol_promoter_sigma54_elementc, bacterial_RNApol_promoter_sigma_70_elementc, bacterial_RNApol_promoter_sigma_ecf_elementc

bacterial_RNApol_promoter_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000843

This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.

bacterial_RNApol_promoter_sigma54_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001672

has super-classes
bacterial_RNApol_promoterc

bacterial_RNApol_promoter_sigma_70_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001671

has super-classes
bacterial_RNApol_promoterc

bacterial_RNApol_promoter_sigma_ecf_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001913

Requested by Kevin Clancy - invitrogen -May 2012.
has super-classes
bacterial_RNApol_promoterc

bacterial_terminatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000614

Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.
has super-classes
terminatorc
has sub-classes
rho_dependent_bacterial_terminatorc, rho_independent_bacterial_terminatorc

basec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001236

has super-classes
biological_regionc
has sub-classes
modified_DNA_basec, modified_RNA_base_featurec

base_call_error_correctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001526

has super-classes
sequence_differencec

base_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000028

has super-classes
sequence_secondary_structurec
has sub-classes
Hoogsteen_base_pairc, WC_base_pairc, reverse_Hoogsteen_base_pairc, sugar_edge_base_pairc, wobble_base_pairc

Bel_Pao_LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002266

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LTR_retrotransposonc

benign_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001770

has super-classes
variant_phenotypec

beta_bulgec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001107

has super-classes
polypeptide_secondary_structurec

beta_bulge_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001108

has super-classes
polypeptide_secondary_structurec
has sub-classes
beta_bulge_loop_fivec, beta_bulge_loop_sixc

beta_bulge_loop_fivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001109

has super-classes
beta_bulge_loopc

beta_bulge_loop_sixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001110

has super-classes
beta_bulge_loopc

beta_strandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001111

Range.
has super-classes
polypeptide_secondary_structurec
has sub-classes
antiparallel_beta_strandc, parallel_beta_strandc

beta_turnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001133

has super-classes
polypeptide_turn_motifc
has sub-classes
beta_turn_left_handed_type_onec, beta_turn_left_handed_type_twoc, beta_turn_right_handed_type_onec, beta_turn_right_handed_type_twoc, beta_turn_type_eightc, beta_turn_type_sixc

beta_turn_left_handed_type_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001134

has super-classes
beta_turnc

beta_turn_left_handed_type_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001135

has super-classes
beta_turnc

beta_turn_right_handed_type_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001136

has super-classes
beta_turnc

beta_turn_right_handed_type_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001137

has super-classes
beta_turnc

beta_turn_type_eightc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001155

has super-classes
beta_turnc

beta_turn_type_sixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001150

has super-classes
beta_turnc
has sub-classes
beta_turn_type_six_ac, beta_turn_type_six_bc

beta_turn_type_six_ac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001151

has super-classes
beta_turn_type_sixc
has sub-classes
beta_turn_type_six_a_onec, beta_turn_type_six_a_twoc

beta_turn_type_six_a_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001152

has super-classes
beta_turn_type_six_ac

beta_turn_type_six_a_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001153

has super-classes
beta_turn_type_six_ac

beta_turn_type_six_bc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001154

has super-classes
beta_turn_type_sixc

bidirectional_gene_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002086

Requested by SNPEFF team. Feb 2016.
has super-classes
gene_fusionc

bidirectional_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000568

Definition updated in Aug 2020 by Dave Sant.
has super-classes
promoterc

bidirectional_promoter_lncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002185

This is a gencode term. See GitHub Issue #408. Synonyms "bidirectional promoter lncRNA gene" and "bidirectional_promoter_lncRNA_gene" added 23 April 2021 by David Sant. See GitHub Issue #506.
has super-classes
lncRNA_genec

binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000409

See GO:0005488 : binding.
has super-classes
biological_regionc
has sub-classes
epitopec, homologous_chromosome_recognition_and_pairing_locusc, ligand_binding_sitec, metal_binding_sitec, nucleotide_binding_sitec, protein_binding_sitec

biochemical_region_of_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100001

Range.
has super-classes
polypeptide_motifc
has sub-classes
conformational_switchc, molecular_contact_regionc, polypeptide_binding_motifc, polypeptide_catalytic_motifc, post_translationally_modified_regionc

biological_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001411

has super-classes
regionc
has sub-classes
CpG_islandc, D_loopc, Okazaki_fragmentc, QTLc, accessible_DNA_regionc, amino_acidc, basec, binding_sitec, capc, chromosome_partc, deletionc, genec, gene_component_regionc, gene_groupc, gene_member_regionc, genetic_markerc, insertionc, intergenic_regionc, inversionc, linkage_groupc, mobile_genetic_elementc, mutational_hotspotc, oligo_U_tailc, open_chromatin_regionc, origin_of_replicationc, polyA_sequencec, polyA_site_clusterc, polypeptidec, polypeptide_regionc, pseudogenec, pseudogenic_regionc, rearrangement_regionc, recombination_featurec, repeat_regionc, repeat_unitc, repliconc, restriction_enzyme_regionc, retronc, sequence_motifc, sequence_secondary_structurec, substitutionc, transcript_regionc, unit_of_gene_expressionc

biomaterial_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001409

has super-classes
regionc
has sub-classes
engineered_regionc, reagentc

bipartite_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000149

has super-classes
interchromosomal_mutationc
intrachromosomal_duplicationc

bipartite_inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000151

has super-classes
chromosomal_inversionc

blocked_reading_framec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000718

Term requested by Rama from SGD.
has super-classes
reading_framec

blunt_end_restriction_enzyme_cleavage_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001693

has super-classes
restriction_enzyme_cleavage_junctionc
part_ofop some blunt_end_restriction_enzyme_cleavage_sitec

blunt_end_restriction_enzyme_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001691

has super-classes
restriction_enzyme_recognition_sitec

bound_by_factorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000277

Formerly called transcript_by_bound_factor.
has super-classes
feature_attributec
has sub-classes
bound_by_nucleic_acidc, bound_by_proteinc

bound_by_nucleic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000876

has super-classes
bound_by_factorc

bound_by_proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000875

has super-classes
bound_by_factorc

boundary_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002020

Requested by Antonia Lock. Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf).
has super-classes
insulatorc

branch_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000611

has super-classes
spliceosomal_intron_regionc

BREd_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001663

has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_II_core_promoterc

BREu_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000016

Binds TFIIB.
has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_II_core_promoterc

Bruno_response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001181

Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
has super-classes
UTR_regionc
part_ofop some three_prime_UTRc

C_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000622

has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_III_promoter_type_1c

C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000558

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some C_gene_segmentc

C_D_box_snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000593

has super-classes
snoRNAc
derives_fromop some C_D_box_snoRNA_primary_transcriptc
has sub-classes
U14_snoRNAc, U3_snoRNAc, methylation_guide_snoRNAc

C_D_box_snoRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000585

has super-classes
snoRNA_encodingc

C_D_box_snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000595

has super-classes
snoRNA_primary_transcriptc

C_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000478

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_segmentc

C_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001834

has super-classes
immunoglobulin_regionc

c_terminal_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100015

has super-classes
cleaved_peptide_regionc
part_ofop some signal_peptidec

C_to_A_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000019

has super-classes
pyrimidine_to_purine_transversionc

C_to_G_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000020

has super-classes
pyrimidine_to_purine_transversionc

C_to_T_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000011

has super-classes
pyrimidine_transitionc
has sub-classes
C_to_T_transition_at_pCpG_sitec

C_to_T_transition_at_pCpG_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000012

has super-classes
C_to_T_transitionc

CAAT_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000172

has super-classes
DNA_motifc
part_ofop some RNApol_II_promoterc

CAAX_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002230

Added as per request by Val Wood GitHub issue #479 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/479)
has super-classes
polypeptide_conserved_motifc

CACTA_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002285

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

CAGE_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001917

has super-classes
transcription_start_clusterc

CAGE_tagc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001916

has super-classes
tagc

candidate_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001867

Requested by Bayer Cropscience December, 2011.
has super-classes
genec
has sub-classes
functional_candidate_genec, positional_candidate_genec

canonical_five_prime_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000677

has super-classes
five_prime_cis_splice_sitec

canonical_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000675

canonical_three_prime_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000676

has super-classes
three_prime_cis_splice_sitec

capc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000581

has super-classes
biological_regionc

cappedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000146

has super-classes
transcript_attributec

capped_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000862

is equivalent to
mRNAc and (adjacent_toop some capc) and (has_qualityop some cappedc)
has super-classes
mRNAc
has_qualityop some cappedc
adjacent_toop some capc

capped_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000861

is equivalent to
primary_transcriptc and (adjacent_toop some capc) and (has_qualityop some cappedc)
has super-classes
primary_transcriptc
adjacent_toop some capc
has_qualityop some cappedc

CArG_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002156

Requested by Antonia Lock
has super-classes
promoter_elementc

cassette_array_memberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005847

has super-classes
gene_cassette_memberc

cassette_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001434

Requested by the Trypanosome community.
has super-classes
non_processed_pseudogenec

catalytic_residuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001104

Discrete.
has super-classes
amino_acidc
part_ofop some polypeptide_catalytic_motifc

catmat_left_handed_fourc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100005

has super-classes
polypeptide_secondary_structurec

catmat_left_handed_threec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100004

has super-classes
polypeptide_secondary_structurec

catmat_right_handed_fourc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100007

has super-classes
polypeptide_secondary_structurec

catmat_right_handed_threec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100006

has super-classes
polypeptide_secondary_structurec

CCA_tailc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001175

has super-classes
tRNA_regionc

CCAAT_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001856

has super-classes
promoter_elementc

cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000756

has super-classes
DNAc
has sub-classes
double_stranded_cDNAc, single_stranded_cDNAc

cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000317

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is equivalent to
clonec and (has_qualityop some cDNAc)
has super-classes
clonec
has_qualityop some cDNAc
has sub-classes
invalidated_cDNA_clonec, three_prime_RACE_clonec, validated_cDNA_clonec

cDNA_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000689

has super-classes
expressed_sequence_matchc

CDRE_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001865

has super-classes
promoter_elementc

CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000316

has super-classes
mRNA_regionc
has sub-classes
CDS_extensionc, CDS_fragmentc, CDS_independently_knownc, CDS_predictedc, edited_CDSc, transposable_element_CDSc

CDS_extensionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002227

Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)
has super-classes
CDSc
has sub-classes
CDS_five_prime_extensionc, CDS_three_prime_extensionc

CDS_five_prime_extensionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002228

Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)
has super-classes
CDS_extensionc

CDS_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001384

is equivalent to
CDSc and (has_qualityop some fragmentaryc)
has super-classes
CDSc
has_qualityop some fragmentaryc

CDS_independently_knownc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001246

is equivalent to
CDSc and (has_qualityop some independently_knownc)
has super-classes
CDSc
has_qualityop some independently_knownc

CDS_predictedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001254

is equivalent to
CDSc and (has_qualityop some predictedc)
has super-classes
CDSc
has_qualityop some predictedc
has sub-classes
CDS_supported_by_sequence_similarity_datac, orphan_CDSc

CDS_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000851

has super-classes
mRNA_regionc
part_ofop some CDSc
has sub-classes
coding_endc, coding_startc, codonc, mature_protein_region_of_CDSc, propeptide_region_of_CDSc, signal_peptide_region_of_CDSc, transit_peptide_region_of_CDSc

CDS_supported_by_domain_match_datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001249

is equivalent to
CDS_supported_by_sequence_similarity_datac and (has_qualityop some supported_by_domain_matchc)
has super-classes
CDS_supported_by_sequence_similarity_datac
has_qualityop some supported_by_domain_matchc

CDS_supported_by_EST_or_cDNA_datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001259

is equivalent to
CDS_supported_by_sequence_similarity_datac and (has_qualityop some supported_by_EST_or_cDNAc)
has super-classes
CDS_supported_by_sequence_similarity_datac
has_qualityop some supported_by_EST_or_cDNAc

CDS_supported_by_peptide_spectrum_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002071

has super-classes
CDS_supported_by_sequence_similarity_datac

CDS_supported_by_sequence_similarity_datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001251

is equivalent to
CDSc and (has_qualityop some supported_by_sequence_similarityc)
has super-classes
CDS_predictedc
has_qualityop some supported_by_sequence_similarityc
has sub-classes
CDS_supported_by_EST_or_cDNA_datac, CDS_supported_by_domain_match_datac, CDS_supported_by_peptide_spectrum_matchc

CDS_three_prime_extensionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002229

Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)
has super-classes
CDS_extensionc

central_hydrophobic_region_of_signal_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100016

has super-classes
cleaved_peptide_regionc
part_ofop some signal_peptidec

centromerec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000577

has super-classes
chromosomal_structural_elementc
has sub-classes
point_centromerec, regional_centromerec

centromere_DNA_Element_Ic back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001493

This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
has super-classes
conserved_regionc
part_ofop some point_centromerec

centromere_DNA_Element_IIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001494

This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
has super-classes
conserved_regionc
part_ofop some point_centromerec

centromere_DNA_Element_IIIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001495

This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
has super-classes
conserved_regionc
part_ofop some point_centromerec

centromeric_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001797

has super-classes
repeat_regionc
has sub-classes
dg_repeatc, dh_repeatc, regional_centromere_inner_repeat_regionc, regional_centromere_outer_repeat_regionc

chimeric_cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000810

is equivalent to
invalidated_cDNA_clonec and (has_qualityop some invalidated_by_chimeric_cDNAc)
has super-classes
invalidated_cDNA_clonec
has_qualityop some invalidated_by_chimeric_cDNAc

ChIP_seq_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001697

has super-classes
experimentally_defined_binding_regionc
containsop some protein_binding_sitec

chloroplast_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000820

is equivalent to
chromosomec and (has_originop some chloroplast_sequencec)
has super-classes
chromosomec
has_originop some chloroplast_sequencec

chloroplast_DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001033

This term is used by MO.
is equivalent to
chloroplast_sequencec and (has_qualityop some DNAc)
has super-classes
chloroplast_sequencec
has_qualityop some DNAc

chloroplast_DNA_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001930

Requested by Bayer Cropscience, October, 2012.
is equivalent to
readc and (has_originop some chloroplast_DNAc)
has super-classes
readc
has_originop some chloroplast_DNAc

chloroplast_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000745

has super-classes
plastid_sequencec
has sub-classes
chloroplast_DNAc

chromatin_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002306

Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
has super-classes
chromosome_partc

chromoplast_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000821

is equivalent to
chromosomec and (has_originop some chromoplast_sequencec)
has super-classes
chromosomec
has_originop some chromoplast_sequencec

chromoplast_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000093

is equivalent to
plastid_genec and (has_originop some chromoplast_sequencec)
has super-classes
plastid_genec
has_originop some chromoplast_sequencec

chromoplast_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000744

has super-classes
plastid_sequencec

chromosomal_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000029

is equivalent to
intrachromosomal_mutationc and (has_partop some deletionc)
has super-classes
intrachromosomal_mutationc
has_partop some deletionc
has sub-classes
deficient_intrachromosomal_transpositionc, deficient_inversionc, deficient_translocationc, inversion_derived_bipartite_deficiencyc, inversion_derived_deficiency_plus_aneuploidc, inversion_derived_deficiency_plus_duplicationc

chromosomal_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000037

has super-classes
chromosome_structure_variationc
has sub-classes
free_duplicationc, insertional_duplicationc, interchromosomal_duplicationc, intrachromosomal_duplicationc

chromosomal_inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000030

is equivalent to
intrachromosomal_mutationc and (has_partop some inversionc)
has super-classes
intrachromosomal_mutationc
has_partop some inversionc
has sub-classes
bipartite_inversionc, deficient_inversionc, inversion_cum_translocationc, inverted_ring_chromosomec, paracentric_inversionc, pericentric_inversionc

chromosomal_regulatory_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000626

has super-classes
chromosome_partc
has sub-classes
matrix_attachment_sitec

chromosomal_structural_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000628

has super-classes
chromosome_partc
has sub-classes
centromerec, subtelomerec, telomerec

chromosomal_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000044

has super-classes
translocationc
interchromosomal_mutationc
has sub-classes
Robertsonian_fusionc, deficient_translocationc, interchromosomal_translocationc, intrachromosomal_translocationc, inversion_cum_translocationc, reciprocal_chromosomal_translocationc, translocation_elementc

chromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000453

has super-classes
chromosome_structure_variationc
has sub-classes
interchromosomal_transpositionc, intrachromosomal_transpositionc

chromosomal_variation_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001509

has super-classes
alteration_attributec
has sub-classes
interchromosomalc, intrachromosomalc

chromosomally_aberrant_genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001524

has super-classes
variant_genomec

chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000340

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
repliconc
has sub-classes
DNA_chromosomec, RNA_chromosomec, apicoplast_chromosomec, chloroplast_chromosomec, chromoplast_chromosomec, cyanelle_chromosomec, leucoplast_chromosomec, macronuclear_chromosomec, micronuclear_chromosomec, mitochondrial_chromosomec, nuclear_chromosomec, nucleomorphic_chromosomec

chromosome_armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000105

has super-classes
chromosome_partc

chromosome_bandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000341

has super-classes
chromosome_partc

chromosome_breakage_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000670

has super-classes
sequence_rearrangement_featurec

chromosome_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001021

has super-classes
junctionc
part_ofop some chromosomec
has sub-classes
deletion_breakpointc, insertion_breakpointc, interchromosomal_breakpointc, intrachromosomal_breakpointc, inversion_breakpointc, translocation_breakpointc

chromosome_fissionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000141

has super-classes
intrachromosomal_mutationc

chromosome_number_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000182

has super-classes
chromosome_variationc
has sub-classes
aneuploidc, polyploidc

chromosome_partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000830

This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
has super-classes
biological_regionc
part_ofop some chromosomec
has sub-classes
Crick_strandc, DNA_loopc, Watson_strandc, chromatin_regulatory_regionc, chromosomal_regulatory_elementc, chromosomal_structural_elementc, chromosome_armc, chromosome_bandc, interbandc, introgressed_chromosome_regionc

chromosome_structure_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000183

has super-classes
chromosome_variationc
has sub-classes
aneuploid_chromosomec, autosynaptic_chromosomec, chromosomal_duplicationc, chromosomal_transpositionc, complex_structural_alterationc, compound_chromosomec, free_chromosome_armc, interchromosomal_mutationc, intrachromosomal_mutationc, uncharacterized_chromosomal_mutationc

chromosome_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000240

has super-classes
variant_collectionc
part_ofop some chromosomally_aberrant_genomec
has sub-classes
assortment_derived_variationc, chromosome_number_variationc, chromosome_structure_variationc

circularc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000988

Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
has super-classes
topology_attributec
is disjoint with
linearc

circular_double_stranded_DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000958

is equivalent to
double_stranded_DNA_chromosomec and (has_qualityop some circularc)
has super-classes
double_stranded_DNA_chromosomec
has_qualityop some circularc

circular_double_stranded_RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000967

is equivalent to
double_stranded_RNA_chromosomec and (has_qualityop some circularc)
has super-classes
double_stranded_RNA_chromosomec
has_qualityop some circularc

circular_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002292

Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)
has super-classes
mRNAc

circular_ncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002291

Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)
has super-classes
ncRNAc

circular_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002211

has super-classes
plasmidc

circular_single_stranded_DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000960

is equivalent to
single_stranded_DNA_chromosomec and (has_qualityop some circularc)
has super-classes
single_stranded_DNA_chromosomec
has_qualityop some circularc

circular_single_stranded_RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000966

is equivalent to
single_stranded_RNA_chromosomec and (has_qualityop some circularc)
has super-classes
single_stranded_RNA_chromosomec
has_qualityop some circularc

cis_acting_homologous_chromosome_pairing_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002025

Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase.
has super-classes
DNA_motifc

cis_regulatory_frameshift_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001427

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc

cis_regulatory_modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000727

Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.
has super-classes
transcriptional_cis_regulatory_regionc
has sub-classes
DNA_loop_anchorc, enhancerc, insulatorc, locus_control_regionc, silencerc

cis_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001419

has super-classes
splice_sitec
has sub-classes
extended_cis_splice_sitec, five_prime_cis_splice_sitec, recursive_splice_sitec, three_prime_cis_splice_sitec

class_I_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000990

Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
has super-classes
ncRNAc

class_II_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000989

has super-classes
ncRNAc

cleaved_for_gpi_anchor_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001408

has super-classes
cleaved_peptide_regionc

cleaved_initiator_methioninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000691

has super-classes
cleaved_peptide_regionc

cleaved_peptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100011

Range.
has super-classes
polypeptide_regionc
part_ofop some immature_peptide_regionc
has sub-classes
c_terminal_regionc, central_hydrophobic_region_of_signal_peptidec, cleaved_for_gpi_anchor_regionc, cleaved_initiator_methioninec, inteinc, lipoprotein_signal_peptidec, n_terminal_regionc, propeptidec, propeptide_cleavage_sitec

clipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000303

has super-classes
primary_transcript_regionc
has sub-classes
five_prime_clipc, three_prime_clipc

clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000151

has super-classes
reagentc
has sub-classes
cDNA_clonec, genomic_clonec, tiling_path_clonec

clone_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000787

clone_endc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001793

has super-classes
readc
part_ofop some clonec

clone_insertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000753

has super-classes
reagentc
part_ofop some clonec
has sub-classes
cloned_cDNA_insertc, cloned_genomic_insertc, engineered_insertc

clone_insert_endc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000103

has super-classes
junctionc
part_ofop some clone_insertc

clone_insert_startc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000179

has super-classes
junctionc
part_ofop some clone_insertc

clone_insert_startc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000767

clonedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000788

cloned_cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000792

cloned_cDNA_insertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000913

is equivalent to
clone_insertc and (has_qualityop some cDNAc)
has super-classes
clone_insertc
has_qualityop some cDNAc

cloned_genomicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000791

cloned_genomic_insertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000914

is equivalent to
clone_insertc and (has_qualityop some genomic_DNAc)
has super-classes
clone_insertc
has_qualityop some genomic_DNAc
has sub-classes
BAC_cloned_genomic_insertc

cloned_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000785

Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
has super-classes
reagentc
part_ofop some clone_insertc

coding_conserved_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000332

has super-classes
conserved_regionc

coding_endc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000327

has super-classes
CDS_regionc

coding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000195

has super-classes
exonc
has sub-classes
five_prime_coding_exonc, interior_coding_exonc, three_prime_coding_exonc

coding_region_of_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001215

An exon containing either a start or stop codon will be partially coding and partially non coding.
has super-classes
exon_regionc
has sub-classes
five_prime_coding_exon_coding_regionc, three_prime_coding_exon_coding_regionc

coding_sequence_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001580

has super-classes
exon_variantc
coding_transcript_variantc
has sub-classes
initiator_codon_variantc, protein_altering_variantc, synonymous_variantc, terminator_codon_variantc

coding_startc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000323

has super-classes
CDS_regionc

coding_transcript_intron_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001969

has super-classes
intron_variantc
coding_transcript_variantc
has sub-classes
3_prime_UTR_intron_variantc, 5_prime_UTR_intron_variantc

coding_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001968

has super-classes
transcript_variantc
has sub-classes
UTR_variantc, coding_sequence_variantc, coding_transcript_intron_variantc

coding_transcript_with_retained_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002112

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
protein_coding_primary_transcriptc

coding_variant_qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001814

has super-classes
variant_qualityc
has sub-classes
non_synonymousc, synonymousc

codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000360

has super-classes
CDS_regionc
has sub-classes
recoded_codonc, start_codonc, stop_codonc

codon_redefinedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000882

has super-classes
recodedc

coiled_coilc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001080

Range.
has super-classes
polypeptide_structural_motifc

cointegrated_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001045

has super-classes
integrated_mobile_genetic_elementc

common_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001767

has super-classes
variant_frequencyc

compensatory_transcript_secondary_structure_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001597

has super-classes
transcript_secondary_structure_variantc

complex_3D_structural_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001600

has super-classes
3D_polypeptide_structure_variantc

complex_change_of_translational_product_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001602

has super-classes
translational_product_function_variantc

complex_chromosomal_rearrangementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002062

has super-classes
complex_structural_alterationc

complex_operonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002299

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
operonc

complex_regulonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002303

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
regulonc

complex_structural_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001784

has super-classes
structural_alterationc
chromosome_structure_variationc
has sub-classes
complex_chromosomal_rearrangementc

complex_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000005

has super-classes
substitutionc

complex_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001577

EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
has super-classes
transcript_variantc

compositionally_biased_region_of_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001066

Range.
has super-classes
polypeptide_regionc

compound_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000042

has super-classes
chromosome_structure_variationc
has sub-classes
compound_chromosome_armc, hetero_compound_chromosomec, homo_compound_chromosomec

compound_chromosome_armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000060

FLAG - this term is should probably be a part of rather than an is_a.
has super-classes
compound_chromosomec

computed_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000309

computed_feature_by_similarityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000311

similar to:<sequence_id>

conformational_change_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001601

has super-classes
3D_polypeptide_structure_variantc

conformational_switchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001422

MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
has super-classes
biochemical_region_of_peptidec

conjugative_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000371

has super-classes
DNA_transposonc

consensusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000993

Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
has super-classes
statusc

consensus_AFLP_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001991

Requested by Bayer Cropscience September, 2013.
has super-classes
consensus_regionc

consensus_gDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001931

Requested by Bayer Cropscience November, 2012.
has super-classes
consensus_regionc

consensus_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000995

DO not obsolete without considering MGED mapping.
is equivalent to
mRNAc and (has_qualityop some consensusc)
has super-classes
mRNAc
consensus_regionc
has_qualityop some consensusc

consensus_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000994

DO not obsolete without considering MGED mapping.
is equivalent to
regionc and (has_qualityop some consensusc)
has super-classes
experimental_featurec
has_qualityop some consensusc
has sub-classes
consensus_AFLP_fragmentc, consensus_gDNAc, consensus_mRNAc

conservative_amino_acid_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001607

has super-classes
amino_acid_substitutionc

conservative_inframe_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001825

has super-classes
inframe_deletionc

conservative_inframe_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001823

has super-classes
inframe_insertionc

conservative_missense_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001585

has super-classes
missense_variantc

conservedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000856

has super-classes
feature_attributec
has sub-classes
homologousc, syntenicc

conserved_intergenic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002017

Requested by Uma Paila (UVA) for snpEff.
has super-classes
intergenic_variantc

conserved_intron_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002018

Requested by Uma Paila (UVA) for snpEff.
has super-classes
intron_variantc

conserved_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000330

has super-classes
experimental_featurec
has sub-classes
RR_tractc, U_boxc, X_elementc, centromere_DNA_Element_Ic, centromere_DNA_Element_IIc, centromere_DNA_Element_IIIc, coding_conserved_regionc, homologous_regionc, nc_conserved_regionc, regional_centromere_central_corec, syntenic_regionc

constitutive_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002050

has super-classes
promoterc

contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000149

has super-classes
assembly_componentc
sequence_assemblyc
part_ofop some supercontigc
has sub-classes
BAC_read_contigc, genomic_DNA_contigc, mRNA_contigc, mitochondrial_contigc

contig_collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001462

See tracker ID: 2138359.
is equivalent to
sequence_conflictc and (has_partop some contigc)
has super-classes
sequence_conflictc
sequence_collectionc
has_partop some contigc

contig_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000476

has super-classes
readc

Copia_LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002264

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LTR_retrotransposonc

copy_number_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001563

has super-classes
sequence_length_variantc
has sub-classes
copy_number_decreasec, copy_number_increasec

copy_number_decreasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001912

has super-classes
copy_number_changec

copy_number_gainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001742

has super-classes
copy_number_variationc

copy_number_increasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001911

has super-classes
copy_number_changec

copy_number_lossc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001743

has super-classes
copy_number_variationc

copy_number_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001019

has super-classes
sequence_length_alterationc
has sub-classes
copy_number_gainc, copy_number_lossc, presence_absence_variationc

core_eukaryotic_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001660

has super-classes
core_promoter_elementc
part_ofop some eukaryotic_promoterc
has sub-classes
AACCCT_boxc, A_boxc, BREd_motifc, BREu_motifc, B_boxc, C_boxc, DCEc, DPE_motifc, INR_motifc, MTEc, TATA_boxc, TCT_motifc, homol_D_boxc, intermediate_elementc

core_prokaryotic_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002312

has super-classes
core_promoter_elementc
part_ofop some prokaryotic_promoterc

core_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002309

Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
has super-classes
promoter_elementc
part_ofop some promoterc
has sub-classes
TSSc, core_eukaryotic_promoter_elementc, core_prokaryotic_promoter_elementc, core_viral_promoter_elementc

core_viral_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002313

has super-classes
core_promoter_elementc
part_ofop some viral_promoterc

cosmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000156

Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
vector_repliconc

cosmid_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000765

covalent_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001090

CpG_islandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000307

has super-classes
biological_regionc

CREc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001843

New synonym Atf1/Pcr1 recognition motif added in response to Antonia Lock GitHub Issue Request #437, PMID:15716492
has super-classes
promoter_elementc

Crick_strandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002263

Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419)
has super-classes
chromosome_partc

CRISPRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001459

has super-classes
direct_repeatc

cross_genome_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000177

has super-classes
nucleotide_matchc

cross_linkc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001087

crypticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000976

has super-classes
feature_attributec

cryptic_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001431

is equivalent to
genec and (has_qualityop some crypticc)
has super-classes
genec
has_qualityop some crypticc
has sub-classes
cryptogenec

cryptic_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002310

Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
has super-classes
promoterc
part_ofop some cryptic_genec

cryptic_prophagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001007

This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
has super-classes
genomic_islandc

cryptic_splice_acceptorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001570

has super-classes
cryptic_splice_site_variantc

cryptic_splice_donorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001571

has super-classes
cryptic_splice_site_variantc

cryptic_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001533

has super-classes
splice_sitec

cryptic_splice_site_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001569

has super-classes
splicing_variantc
has sub-classes
cryptic_splice_acceptorc, cryptic_splice_donorc

cryptogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001196

is equivalent to
maxicircle_genec and (has_qualityop some crypticc)
has super-classes
maxicircle_genec
cryptic_genec
has_qualityop some crypticc

Crypton_YR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002277

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
DNA_transposonc

CSL_response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001839

has super-classes
promoter_elementc

CsrB_RsmB_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000377

has super-classes
small_regulatory_ncRNAc

ct_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000092

is equivalent to
plastid_genec and (has_originop some chloroplast_sequencec)
has super-classes
plastid_genec
has_originop some chloroplast_sequencec

CTCF_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001974

has super-classes
promoter_elementc

CTG_start_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001273

has super-classes
non_canonical_start_codonc

CuREc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001844

has super-classes
promoter_elementc

cyanelle_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000822

is equivalent to
chromosomec and (has_originop some cyanelle_sequencec)
has super-classes
chromosomec
has_originop some cyanelle_sequencec

cyanelle_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000094

is equivalent to
plastid_genec and (has_originop some cyanelle_sequencec)
has super-classes
plastid_genec
has_originop some cyanelle_sequencec

cyanelle_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000746

has super-classes
plastid_sequencec

cyclic_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000150

has super-classes
interchromosomal_translocationc

cysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001447

A place holder for a cross product with chebi.
has super-classes
amino_acidc

cysteine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000215

has super-classes
tRNA_primary_transcriptc

cysteinyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000258

has super-classes
tRNAc
derives_fromop some cysteine_tRNA_primary_transcriptc

cytoplasmic_polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001073

has super-classes
extramembrane_polypeptide_regionc

cytosolic_16S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001000

Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
has super-classes
cytosolic_SSU_rRNAc

cytosolic_18S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000407

Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
has super-classes
cytosolic_SSU_rRNAc

cytosolic_23S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001001

Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
has super-classes
cytosolic_LSU_rRNAc

cytosolic_25S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001002

Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
has super-classes
cytosolic_LSU_rRNAc

cytosolic_28S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000653

Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
has super-classes
cytosolic_LSU_rRNAc

cytosolic_2S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002337

Added as a request from FlyBase. See GitHub Issue #507. Renamed from rRNA_2S to cytosolic_2S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
has super-classes
cytosolic_LSU_rRNAc

cytosolic_5_8S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000375

Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
has super-classes
cytosolic_LSU_rRNAc

cytosolic_5S_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000652

Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
has super-classes
cytosolic_LSU_rRNAc

cytosolic_LSU_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000651

Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
has super-classes
cytosolic_rRNAc
derives_fromop some rRNA_large_subunit_primary_transcriptc
has sub-classes
cytosolic_23S_rRNAc, cytosolic_25S_rRNAc, cytosolic_28S_rRNAc, cytosolic_2S_rRNAc, cytosolic_5S_rRNAc, cytosolic_5_8S_rRNAc

cytosolic_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002343

Added as a request from EBI. See GitHub Issue #493
has super-classes
rRNAc
has sub-classes
cytosolic_LSU_rRNAc, cytosolic_SSU_rRNAc

cytosolic_SSU_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000650

Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
has super-classes
cytosolic_rRNAc
derives_fromop some rRNA_small_subunit_primary_transcriptc
has sub-classes
cytosolic_16S_rRNAc, cytosolic_18S_rRNAc

D_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000559

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some D_gene_segmentc

D_DJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000504

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some DJ_gene_segmentc
has_partop some D_gene_segmentc
has_partop some C_gene_segmentc

D_DJ_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000505

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some D_gene_segmentc
has_partop some DJ_gene_segmentc

D_DJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000506

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some J_gene_segmentc
has_partop some DJ_gene_segmentc
has_partop some D_gene_segmentc
has_partop some C_gene_segmentc

D_DJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000508

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some D_gene_segmentc
has_partop some J_gene_segmentc
has_partop some DJ_gene_segmentc

D_gene_recombination_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000492

has super-classes
vertebrate_immune_system_gene_recombination_signal_featurec
has sub-classes
five_prime_D_recombination_signal_sequencec, three_prime_D_recombination_signal_sequencec

D_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000458

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_segmentc

D_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000509

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some D_gene_segmentc
has_partop some J_gene_segmentc
has_partop some C_gene_segmentc

D_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000560

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some D_gene_segmentc
has_partop some J_gene_segmentc

D_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000297

Moved from is_a: SO:0000296 origin_of_replication to is_a: SO:0001411 biological_region after Terrence Murphy (INSDC) pointed out that the D loop can also refer to a loop in DNA repair, which is not an origin of replication. See GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)
has super-classes
biological_regionc
has sub-classes
mitochondrial_D_loopc

DArT_markerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001646

has super-classes
genetic_markerc

databank_entryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_2000061

has super-classes
reagentc

dCAPS_primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001699

has super-classes
primerc

DCEc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001664

has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_II_core_promoterc

DCE_SIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001665

has super-classes
DNA_motifc
part_ofop some DCEc

DCE_SIIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001666

has super-classes
DNA_motifc
part_ofop some DCEc

DCE_SIIIc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001667

has super-classes
DNA_motifc
part_ofop some DCEc

DDB_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001804

Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
has super-classes
protein_protein_contactc

de_novo_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001781

has super-classes
variant_originc

decayed_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000464

Does not have to be part of a pseudogene.
has super-classes
pseudogenic_regionc
non_functional_homolog_ofop some exonc

decreased_gene_product_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002316

Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
has super-classes
altered_gene_product_levelc
has sub-classes
absent_gene_productc

decreased_polyadenylation_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001803

Term requested by M. Dumontier, June 1 2011.
has super-classes
polyadenylation_variantc

decreased_transcript_level_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001541

has super-classes
level_of_transcript_variantc

decreased_transcript_stability_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001547

has super-classes
transcript_stability_variantc

decreased_transcription_rate_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001552

has super-classes
rate_of_transcription_variantc

decreased_translational_product_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001555

has super-classes
translational_product_level_variantc

defective_conjugative_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001049

has super-classes
genomic_islandc

deficient_interchromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000063

has super-classes
interchromosomal_transpositionc

deficient_intrachromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000062

has super-classes
chromosomal_deletionc
intrachromosomal_transpositionc
has_partop some deletionc

deficient_inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000171

has super-classes
chromosomal_deletionc
chromosomal_inversionc
has_partop some inversionc
has_partop some deletionc

deficient_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000147

has super-classes
chromosomal_deletionc
chromosomal_translocationc
has_partop some deletionc

deletec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000045

delete_Uc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000918

The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.

deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000159

has super-classes
sequence_alterationc
biological_regionc
has sub-classes
mobile_element_deletionc

deletion_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002174

has super-classes
sequence_alteration_artifactc

deletion_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001415

has super-classes
chromosome_breakpointc

deletion_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000687

has super-classes
junctionc

delinsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000032

Indels can have a different number of bases than the corresponding reference sequence. The term name was changed from indel to delins on 2/24/2019 to align with the HGVS nomenclature term for a deletion-insertion. Indel was causing confusion in the annotation community (github issue 445). The HGVS nomenclature definition of deletion-insertion (delins) is a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion.
has super-classes
sequence_alterationc

designed_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000546

has super-classes
synthetic_sequencec

destruction_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001805

has super-classes
polypeptide_conserved_motifc

dextrosynaptic_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000142

Corrected spelling from dexstrosynaptic_chromosome to dextrosynaptic_chromosome on April 14, 2020 in response to GitHub request #447
has super-classes
autosynaptic_chromosomec

dg_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001898

For the S. pombe project - requested by Val Wood.
has super-classes
centromeric_repeatc
part_ofop some regional_centromere_outer_repeat_regionc

dh_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001899

For the S. pombe project - requested by Val Wood.
has super-classes
centromeric_repeatc
part_ofop some regional_centromere_outer_repeat_regionc

DHU_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001176

has super-classes
tRNA_regionc

dicistronicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000879

has super-classes
polycistronicc

dicistronic_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000716

is equivalent to
mRNAc and (has_qualityop some dicistronicc)
has super-classes
dicistronic_transcriptc
polycistronic_mRNAc
has_qualityop some dicistronicc

dicistronic_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001197

is equivalent to
primary_transcriptc and (has_qualityop some dicistronicc)
has super-classes
dicistronic_transcriptc
polycistronic_primary_transcriptc
has_qualityop some dicistronicc

dicistronic_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000079

is equivalent to
transcriptc and (has_qualityop some dicistronicc)
has super-classes
polycistronic_transcriptc
has_qualityop some dicistronicc
has sub-classes
dicistronic_mRNAc, dicistronic_primary_transcriptc

dif_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000949

has super-classes
resolution_sitec

dihydrouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001228

has super-classes
modified_uridinec

dinucleotide_repeat_microsatellite_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000290

has super-classes
microsatellitec
has sub-classes
GT_dinucleotide_repeatc

diplotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001028

has super-classes
variant_collectionc

directc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001514

has super-classes
insertion_attributec

direct_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000314

has super-classes
repeat_regionc
has sub-classes
CRISPRc, target_site_duplicationc

direct_tandem_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000039

has super-classes
tandem_duplicationc

direction_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001029

has super-classes
feature_attributec
has sub-classes
forwardc, reversec

DIRS_YR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002287

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
YR_retrotransposonc

disabled_reading_framec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002048

has super-classes
reading_framec

disease_associated_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001771

has super-classes
variant_phenotypec

disease_causing_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001772

has super-classes
variant_phenotypec

dispersed_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000658

has super-classes
repeat_regionc

disruptive_inframe_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001826

has super-classes
inframe_deletionc

disruptive_inframe_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001824

has super-classes
inframe_insertionc

distal_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001928

This term is used by Complete Genomics in the structural variant analysis files.
has super-classes
duplicationc

distal_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001670

has super-classes
regulatory_promoter_elementc

distant_three_prime_recoding_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001287

has super-classes
three_prime_recoding_sitec

disulfide_bondc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001088

2 discreet & joined.

DJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000539

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some DJ_gene_segmentc
has_partop some C_gene_segmentc

DJ_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000572

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segmentc

DJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000540

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some DJ_gene_segmentc
has_partop some J_gene_segmentc
has_partop some C_gene_segmentc

DJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000485

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some DJ_gene_segmentc
has_partop some J_gene_segmentc

DMv1_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001165

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

DMv2_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001161

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

DMv3_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001160

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

DMv4_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001157

has super-classes
promoter_elementc

DMv5_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001159

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000352

has super-classes
nucleic_acidc
has sub-classes
cDNAc, genomic_DNAc

DNA_aptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000032

has super-classes
aptamerc

DNA_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001429

has super-classes
nucleotide_binding_sitec
has sub-classes
polypeptide_DNA_contactc, zinc_finger_binding_sitec

DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000954

is equivalent to
chromosomec and (has_qualityop some DNAc)
has super-classes
chromosomec
has_qualityop some DNAc
has sub-classes
double_stranded_DNA_chromosomec, single_stranded_DNA_chromosomec

DNA_constraint_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001009

has super-classes
ds_oligoc

DNA_invertase_target_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000660

DNA_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002307

Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.
has super-classes
chromosome_partc
overlapsop some topologically_associated_domainc

DNA_loop_anchorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002308

Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.
has super-classes
cis_regulatory_modulec
part_ofop some DNA_loopc

DNA_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000713

has super-classes
nucleotide_motifc
has sub-classes
ARS_consensus_sequencec, CAAT_signalc, DCE_SIc, DCE_SIIc, DCE_SIIIc, DRE_motifc, DSR_motifc, E_box_motifc, GAGA_motifc, INR1_motifc, PSE_motifc, Sap1_recognition_motifc, Zas1_recognition_motifc, androgen_response_elementc, cis_acting_homologous_chromosome_pairing_regionc, mating_type_region_motifc, mating_type_region_replication_fork_barrierc, minus_10_signalc, minus_12_signalc, minus_24_signalc, minus_35_signalc, octamer_motifc, promoter_elementc, rDNA_intergenic_spacer_elementc, rDNA_replication_fork_barrierc, teb1_recognition_motifc

DNA_replication_modec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000971

This has been obsoleted as it represents a process. replaced_by: GO:0006260.

DNA_sequence_secondary_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000142

has super-classes
sequence_secondary_structurec
has sub-classes
i_motifc

DNA_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000182

has super-classes
transposable_elementc
has sub-classes
Crypton_YR_transposonc, conjugative_transposonc, foldback_elementc, helitronc, terminal_inverted_repeat_elementc

DNaseI_hypersensitive_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000685

has super-classes
nuclease_hypersensitive_sitec

DNAzymec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001012

Added by request from Colin Batchelor.
is equivalent to
oligoc and (has_qualityop some enzymaticc)
has super-classes
oligoc
has_qualityop some enzymaticc

dominant_negative_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002052

Requested by Deanna Church.
has super-classes
functionally_abnormalc

doublec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000985

Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
has super-classes
strand_attributec

double_stranded_cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000758

has super-classes
cDNAc

double_stranded_DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000955

is equivalent to
DNA_chromosomec and (has_qualityop some doublec)
has super-classes
DNA_chromosomec
has_qualityop some doublec
has sub-classes
circular_double_stranded_DNA_chromosomec, linear_double_stranded_DNA_chromosomec

double_stranded_RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000965

is equivalent to
RNA_chromosomec and (has_qualityop some doublec)
has super-classes
RNA_chromosomec
has_qualityop some doublec
has sub-classes
circular_double_stranded_RNA_chromosomec, linear_double_stranded_RNA_chromosomec

downstream_gene_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001632

Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
has super-classes
intergenic_variantc
has sub-classes
2KB_downstream_variantc, 500B_downstream_variantc, 5KB_downstream_variantc

downstream_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001987

Requested by Graham Ritchie, EBI/Sanger.
has super-classes
intergenic_variantc

DPE1_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001164

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

DPE_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000015

Binds TAF6, TAF9.
has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_II_core_promoterc

DREc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001845

has super-classes
promoter_elementc

DRE_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001156

This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
has super-classes
DNA_motifc
part_ofop some RNApol_II_promoterc

ds_DNA_viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001198

has super-classes
viral_sequencec

ds_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000442

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
oligoc
has sub-classes
DNA_constraint_sequencec, RNAi_reagentc

ds_RNA_viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001169

has super-classes
viral_sequencec

DSR_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002005

Requested by Antonia Locke, (Pombe).
has super-classes
DNA_motifc

DsrA_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000378

has super-classes
small_regulatory_ncRNAc
has sub-classes
GcvB_RNAc

duplicated_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001758

has super-classes
non_processed_pseudogenec

duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000035

has super-classes
insertionc
has sub-classes
distal_duplicationc, tandem_duplicationc

duplication_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002177

has super-classes
insertion_artifactc

duplication_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001523

has super-classes
alteration_attributec
has sub-classes
freec

dye_terminator_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001423

has super-classes
readc

E_box_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001158

has super-classes
DNA_motifc
part_ofop some RNApol_II_promoterc

early_origin_of_replicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002140

has super-classes
origin_of_replicationc

edit_operationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000916

editedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000116

has super-classes
transcript_attributec

edited_by_A_to_I_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000600

edited_by_C_insertion_and_dinucleotide_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000598

edited_by_C_to_U_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000599

edited_by_G_additionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000601

edited_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000935

is equivalent to
CDSc and (has_qualityop some editedc)
has super-classes
CDSc
has_qualityop some editedc

edited_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000929

is equivalent to
mRNAc and (has_qualityop some editedc)
has super-classes
mRNAc
edited_transcriptc
has_qualityop some editedc

edited_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000873

is equivalent to
transcriptc and (has_qualityop some editedc)
has super-classes
transcriptc
has_qualityop some editedc
has_partop some anchor_binding_sitec
guided_byop some guide_RNAc
has sub-classes
edited_mRNAc, edited_transcript_by_A_to_I_substitutionc

edited_transcript_by_A_to_I_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000874

has super-classes
edited_transcriptc

edited_transcript_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000579

has super-classes
transcript_regionc
has sub-classes
editing_blockc, editing_domainc, pre_edited_regionc, unedited_regionc

editing_blockc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000604

has super-classes
edited_transcript_featurec

editing_domainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000606

has super-classes
edited_transcript_featurec

editing_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001544

has super-classes
transcript_processing_variantc

eight_cutter_restriction_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000251

elongated_in_frame_polypeptide_C_terminalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001612

has super-classes
elongated_polypeptide_C_terminalc

elongated_in_frame_polypeptide_N_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001614

has super-classes
elongated_polypeptide_N_terminalc

elongated_out_of_frame_polypeptide_C_terminalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001613

has super-classes
elongated_polypeptide_C_terminalc

elongated_out_of_frame_polypeptide_N_terminalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001615

has super-classes
elongated_polypeptide_N_terminalc

elongated_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001609

has super-classes
polypeptide_sequence_variantc
has sub-classes
elongated_polypeptide_C_terminalc, elongated_polypeptide_N_terminalc

elongated_polypeptide_C_terminalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001610

has super-classes
elongated_polypeptidec
derives_fromop some CDS_three_prime_extensionc
has sub-classes
elongated_in_frame_polypeptide_C_terminalc, elongated_out_of_frame_polypeptide_C_terminalc

elongated_polypeptide_N_terminalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001611

has super-classes
elongated_polypeptidec
derives_fromop some CDS_five_prime_extensionc
has sub-classes
elongated_in_frame_polypeptide_N_terminal_elongationc, elongated_out_of_frame_polypeptide_N_terminalc

encodes_1_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001188

has super-classes
encodes_alternately_spliced_transcriptsc

encodes_alternate_transcription_start_sitesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001241

has super-classes
gene_attributec

encodes_alternately_spliced_transcriptsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000463

has super-classes
gene_attributec
has sub-classes
encodes_1_polypeptidec, encodes_greater_than_1_polypeptidec

encodes_different_polypeptides_different_stopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001190

has super-classes
encodes_overlapping_peptidesc

encodes_disjoint_polypeptidesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001192

has super-classes
encodes_greater_than_1_polypeptidec

encodes_greater_than_1_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001189

has super-classes
encodes_alternately_spliced_transcriptsc
has sub-classes
encodes_disjoint_polypeptidesc, encodes_overlapping_peptidesc

encodes_overlapping_peptidesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001195

has super-classes
encodes_greater_than_1_polypeptidec
has sub-classes
encodes_different_polypeptides_different_stopc, encodes_overlapping_peptides_different_startc, encodes_overlapping_polypeptides_different_start_and_stopc

encodes_overlapping_peptides_different_startc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001191

has super-classes
encodes_overlapping_peptidesc

encodes_overlapping_polypeptides_different_start_and_stopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001193

has super-classes
encodes_overlapping_peptidesc

end_overlapping_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000072

endogenous_retroviral_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000100

is equivalent to
proviral_genec and (has_originop some endogenous_retroviral_sequencec)
has super-classes
proviral_genec
has_originop some endogenous_retroviral_sequencec

endogenous_retroviral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000903

has super-classes
proviral_locationc

Endogenous_Retrovirus_LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002268

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LTR_retrotransposonc

endonuclease_spliced_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001216

has super-classes
intronc
has sub-classes
archaeal_intronc, tRNA_intronc

endosomal_localization_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001529

has super-classes
peptide_localization_signalc

engineeredc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000783

has super-classes
feature_attributec

engineered_DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000793

engineered_episomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000779

Requested by Lynn Crosby Jan 2006.
is equivalent to
episomec and (has_qualityop some engineeredc)
has super-classes
engineered_plasmidc
episomec
has_qualityop some engineeredc

engineered_foreign_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000281

is equivalent to
engineered_genec and (has_qualityop some engineeredc) and (has_qualityop some foreignc)
has super-classes
engineered_genec
foreign_genec
engineered_foreign_regionc
has_qualityop some engineeredc
has_qualityop some foreignc
has sub-classes
engineered_foreign_transposable_element_genec

engineered_foreign_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000805

is equivalent to
regionc and (has_qualityop some engineeredc) and (has_qualityop some foreignc)
has super-classes
engineered_regionc
has_qualityop some foreignc
has_qualityop some engineeredc
has sub-classes
engineered_foreign_genec, engineered_foreign_repetitive_elementc, engineered_foreign_transposable_elementc

engineered_foreign_repetitive_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000293

is equivalent to
repeat_regionc and (has_qualityop some engineeredc) and (has_qualityop some foreignc)
has super-classes
repeat_regionc
engineered_foreign_regionc
has_qualityop some foreignc
has_qualityop some engineeredc

engineered_foreign_transposable_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000799

is equivalent to
transposable_elementc and (has_qualityop some engineeredc) and (has_qualityop some foreignc)
has super-classes
foreign_transposable_elementc
engineered_transposable_elementc
engineered_foreign_regionc
has_qualityop some engineeredc
has_qualityop some foreignc

engineered_foreign_transposable_element_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000283

is equivalent to
transposable_element_genec and (has_qualityop some engineeredc) and (has_qualityop some foreignc)
has super-classes
transposable_element_genec
engineered_foreign_genec
has_qualityop some engineeredc
has_qualityop some foreignc

engineered_fusion_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000288

is equivalent to
fusion_genec and (has_qualityop some engineeredc)
has super-classes
engineered_genec
fusion_genec
has_qualityop some engineeredc

engineered_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000280

is equivalent to
genec and (has_qualityop some engineeredc)
has super-classes
genec
engineered_regionc
has_qualityop some engineeredc
has sub-classes
engineered_foreign_genec, engineered_fusion_genec

engineered_insertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000915

is equivalent to
clone_insertc and (has_qualityop some engineeredc)
has super-classes
clone_insertc
engineered_regionc
has_qualityop some engineeredc

engineered_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000637

is equivalent to
plasmidc and (has_qualityop some engineeredc)
has super-classes
plasmidc
engineered_regionc
has_qualityop some engineeredc
has sub-classes
engineered_episomec, enhancer_trap_constructc, gene_trap_constructc, promoter_trap_constructc

engineered_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000804

is equivalent to
regionc and (has_qualityop some engineeredc)
has super-classes
biomaterial_regionc
has_qualityop some engineeredc
has sub-classes
engineered_foreign_regionc, engineered_genec, engineered_insertc, engineered_plasmidc, engineered_rescue_regionc, engineered_tagc, engineered_transposable_elementc, signaturec, targeting_vectorc

engineered_rescue_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000794

is equivalent to
rescue_regionc and (has_qualityop some engineeredc)
has super-classes
rescue_regionc
engineered_regionc
has_qualityop some engineeredc

engineered_tagc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000807

is equivalent to
tagc and (has_qualityop some engineeredc)
has super-classes
tagc
engineered_regionc
has_qualityop some engineeredc

engineered_transposable_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000798

is equivalent to
transposable_elementc and (has_qualityop some engineeredc)
has super-classes
transposable_elementc
engineered_regionc
has_qualityop some engineeredc
has sub-classes
engineered_foreign_transposable_elementc

enhanceosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001057

enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000165

An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
has super-classes
cis_regulatory_modulec
has sub-classes
enhancer_bound_by_factorc, shadow_enhancerc

enhancer_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000402

enhancer_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001461

has super-classes
nucleotide_to_protein_binding_sitec
part_ofop some enhancerc
has sub-classes
FREc

enhancer_blocking_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002190

Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf).
has super-classes
insulatorc

enhancer_bound_by_factorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000166

is equivalent to
enhancerc and (has_qualityop some bound_by_factorc)
has super-classes
enhancerc
has_qualityop some bound_by_factorc

enhancer_trap_constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001479

has super-classes
engineered_plasmidc

enhancerRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001870

is equivalent to
ncRNAc and (transcribed_fromop some enhancerc)
has super-classes
ncRNAc
transcribed_fromop some enhancerc

enzymaticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001185

Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
has super-classes
feature_attributec
has sub-classes
ribozymicc

enzymatic_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000372

This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
is equivalent to
transcriptc and (has_qualityop some enzymaticc)
has super-classes
transcriptc
has_qualityop some enzymaticc
has sub-classes
ribozymec

enzymatic_RNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002180

has super-classes
ncRNA_genec
has sub-classes
ribozyme_genec

epigenetically_modifiedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000133

has super-classes
gene_attributec
has sub-classes
allelically_excludedc, genomically_imprintedc, rearranged_at_DNA_levelc

epigenetically_modified_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000898

is equivalent to
genec and (has_qualityop some epigenetically_modifiedc)
has super-classes
genec
epigenetically_modified_regionc
has_qualityop some epigenetically_modifiedc
has sub-classes
allelically_excluded_genec, gene_rearranged_at_DNA_levelc, maternally_imprinted_genec, paternally_imprinted_genec

epigenetically_modified_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001720

Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534.
is equivalent to
biological_regionc and (has_qualityop some epigenetically_modifiedc)
has super-classes
regulatory_regionc
has_qualityop some epigenetically_modifiedc
has sub-classes
epigenetically_modified_genec, epigenomically_modified_regionc, histone_modificationc, imprinting_control_regionc, modified_DNA_basec

epigenomically_modified_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002332

Added as part of GREEKC terms to differentiate between inherited and not inherited epigenetic changes. See GitHub Issue #532.
has super-classes
epigenetically_modified_regionc
has_qualityop some epigenetically_modifiedc

episomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000768

has super-classes
plasmidc
has sub-classes
engineered_episomec

epitopec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001018

Requested by Trish Whetzel.
has super-classes
binding_sitec

epoxyqueuosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001318

has super-classes
seven_deazaguanosinec

ER_retention_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001806

has super-classes
peptide_localization_signalc

ESTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000345

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
tagc
derives_fromop some mRNAc
has sub-classes
RSTc, USTc, five_prime_ESTc, three_prime_ESTc

EST_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000668

has super-classes
expressed_sequence_matchc

eukaryotic_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002221

has super-classes
promoterc
has sub-classes
RNApol_III_promoterc, RNApol_II_promoterc, RNApol_I_promoterc

eukaryotic_terminatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000951

has super-classes
terminatorc
has sub-classes
terminator_of_type_2_RNApol_III_promoterc, transcription_termination_signalc

exemplarc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000864

has super-classes
mRNA_attributec

exemplar_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000734

Added for the MO people.
is equivalent to
mRNAc and (has_qualityop some exemplarc)
has super-classes
mRNAc
has_qualityop some exemplarc

exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000147

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
transcript_regionc
has sub-classes
coding_exonc, exon_of_single_exon_genec, interior_exonc, noncoding_exonc

exon_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000333

has super-classes
junctionc
part_ofop some mature_transcriptc

exon_loss_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001572

has super-classes
splicing_variantc

exon_of_single_exon_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005845

has super-classes
exonc

exon_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000852

has super-classes
transcript_regionc
part_ofop some exonc
has sub-classes
coding_region_of_exonc, exonic_splicing_silencerc, noncoding_region_of_exonc

exon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001791

has super-classes
transcript_variantc
has sub-classes
UTR_variantc, coding_sequence_variantc, non_coding_transcript_exon_variantc

exonic_splice_enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000683

has super-classes
splice_enhancerc

exonic_splice_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002084

has super-classes
splice_region_variantc

exonic_splicing_silencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002058

Requested by Javier Diez Perez.
has super-classes
silencerc
exon_regionc

experimental_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001410

has super-classes
regionc
has sub-classes
assemblyc, assembly_componentc, consensus_regionc, conserved_regionc, experimentally_defined_binding_regionc, high_identity_regionc, low_complexity_regionc, matchc, match_partc, mathematically_defined_repeatc, reading_framec, remarkc, spurious_proteinc, transcribed_clusterc, transcribed_fragmentc, transcription_start_clusterc

experimental_feature_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001684

has super-classes
feature_attributec
has sub-classes
quality_valuec, scorec

experimental_result_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000703

has super-classes
remarkc
has sub-classes
no_outputc, overlapping_feature_setc

experimentally_defined_binding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001696

has super-classes
experimental_featurec
has sub-classes
ChIP_seq_regionc

experimentally_determinedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000312

has super-classes
validatedc

expressed_sequence_assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001428

From tracker [ 2372385 ] expressed_sequence_assembly.
has super-classes
sequence_assemblyc

expressed_sequence_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000102

has super-classes
nucleotide_matchc
has sub-classes
EST_matchc, RST_matchc, UST_matchc, cDNA_matchc

extended_cis_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001993

Added by Andy Menzies (Sanger).
has super-classes
cis_splice_sitec

extended_intronic_splice_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001996

has super-classes
intron_domainc

extended_intronic_splice_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001995

Added by Andy Menzies (Sanger).
has super-classes
splicing_variantc

external_transcribed_spacer_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000640

has super-classes
transcribed_spacer_regionc

extrachromosomal_mobile_genetic_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001038

has super-classes
mobile_genetic_elementc
has sub-classes
natural_plasmidc, natural_transposable_elementc, viral_sequencec

extramembrane_polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001072

Range.
has super-classes
polypeptide_structural_regionc
part_ofop some membrane_structurec
has sub-classes
cytoplasmic_polypeptide_regionc, non_cytoplasmic_polypeptide_regionc

feature_ablationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001879

Created in conjunction with the EBI.
has super-classes
structural_variantc
has sub-classes
regulatory_region_ablationc, transcript_ablationc

feature_amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001880

Created in conjunction with the EBI.
has super-classes
structural_variantc
has sub-classes
regulatory_region_amplificationc, transcript_amplificationc

feature_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000733

has super-classes
sequence_attributec
has sub-classes
alteration_attributec, bound_by_factorc, conservedc, crypticc, direction_attributec, engineeredc, enzymaticc, experimental_feature_attributec, flankedc, foreignc, fusionc, gene_attributec, intermediatec, mobilec, naturalc, recombinationally_rearrangedc, rescuec, retrotransposedc, statusc, strand_attributec, transcript_attributec, transgenicc, wild_typec

feature_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001907

has super-classes
feature_variantc
has sub-classes
internal_feature_elongationc, stop_lostc

feature_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001882

Created in conjunction with the EBI.
has super-classes
structural_variantc
has sub-classes
gene_fusionc, regulatory_region_fusionc, transcript_fusionc, transcript_regulatory_region_fusionc

feature_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001881

Created in conjunction with the EBI.
has super-classes
structural_variantc
has sub-classes
regulatory_region_translocationc, transcript_translocationc

feature_truncationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001906

has super-classes
feature_variantc
has sub-classes
frameshift_truncationc, inframe_deletionc, stop_gainedc

feature_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001878

Created in conjunction with the EBI.
has super-classes
structural_variantc
has sub-classes
feature_elongationc, feature_truncationc, gene_variantc, intergenic_variantc, regulatory_region_variantc, silent_mutationc

fingerprint_mapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001250

has super-classes
fragment_assemblyc
has_partop some restriction_fragmentc

finished_genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001491

has super-classes
whole_genome_sequence_statusc

five_aminomethyl_two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001363

has super-classes
modified_uridinec

five_carbamoylmethyl_two_prime_O_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001368

has super-classes
modified_uridinec

five_carbamoylmethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001367

has super-classes
modified_uridinec

five_carboxyhydroxymethyl_uridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001358

has super-classes
modified_uridinec

five_carboxyhydroxymethyl_uridine_methyl_esterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001359

has super-classes
modified_uridinec

five_carboxymethylaminomethyl_two_prime_O_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001370

has super-classes
modified_uridinec

five_carboxymethylaminomethyl_two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001371

has super-classes
modified_uridinec

five_carboxymethylaminomethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001369

has super-classes
modified_uridinec

five_carboxymethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001374

has super-classes
modified_uridinec

five_formyl_two_prime_O_methylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001293

has super-classes
modified_cytidinec

five_formylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001286

has super-classes
modified_cytidinec

five_hydroxymethylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001292

has super-classes
modified_cytidinec

five_hydroxyuridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001354

has super-classes
modified_uridinec

five_isopentenylaminomethyl_two_prime_O_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001382

has super-classes
modified_uridinec

five_isopentenylaminomethyl_two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001381

has super-classes
modified_uridinec

five_isopentenylaminomethyl_uridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001380

has super-classes
modified_uridinec

five_methoxycarbonylmethyl_two_prime_O_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001361

has super-classes
modified_uridinec

five_methoxycarbonylmethyl_two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001362

has super-classes
modified_uridinec

five_methoxycarbonylmethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001360

has super-classes
modified_uridinec

five_methoxyuridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001355

has super-classes
modified_uridinec

five_methyl_2_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001351

has super-classes
modified_uridinec

five_methylaminomethyl_two_selenouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001366

has super-classes
modified_uridinec

five_methylaminomethyl_two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001365

has super-classes
modified_uridinec

five_methylaminomethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001364

has super-classes
modified_uridinec

five_methylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001282

has super-classes
modified_cytidinec

five_methyldihydrouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001376

has super-classes
modified_uridinec

five_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001344

has super-classes
modified_uridinec

five_prime_cis_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000163

has super-classes
cis_splice_sitec
has sub-classes
canonical_five_prime_splice_sitec, non_canonical_five_prime_splice_sitec

five_prime_clipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000555

has super-classes
clipc

five_prime_coding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000200

has super-classes
coding_exonc

five_prime_coding_exon_coding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000196

has super-classes
coding_region_of_exonc
part_ofop some five_prime_coding_exonc

five_prime_coding_exon_noncoding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000486

has super-classes
noncoding_region_of_exonc
part_ofop some five_prime_coding_exonc

five_prime_D_heptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000496

has super-classes
heptamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some five_prime_D_recombination_signal_sequencec

five_prime_D_nonamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000497

has super-classes
nonamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some five_prime_D_recombination_signal_sequencec

five_prime_D_recombination_signal_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000556

has super-classes
D_gene_recombination_featurec

five_prime_D_spacerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000498

has super-classes
vertebrate_immune_system_gene_recombination_spacerc
part_ofop some five_prime_D_recombination_signal_sequencec

five_prime_duplicated_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002245

Added as per request from the Illumina group
has super-classes
partially_duplicated_transcriptc

five_prime_ESTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001208

has super-classes
ESTc

five_prime_five_prime_overlapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000074

has super-classes
overlappingc

five_prime_flanking_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001416

has super-classes
flanking_regionc

five_prime_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000190

has super-classes
intronc

five_prime_LTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000425

has super-classes
long_terminal_repeatc

five_prime_LTR_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000850

has super-classes
LTR_componentc
part_ofop some five_prime_LTRc
has sub-classes
R_five_prime_LTR_regionc, U3_five_prime_LTR_regionc, U5_five_prime_LTR_regionc

five_prime_noncoding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000445

has super-classes
noncoding_exonc

five_prime_open_reading_framec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000629

has super-classes
mRNA_regionc
part_ofop some five_prime_UTRc

five_prime_recoding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001280

has super-classes
recoding_stimulatory_regionc

five_prime_restriction_enzyme_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001689

has super-classes
single_strand_restriction_enzyme_cleavage_sitec
part_ofop some sticky_end_restriction_enzyme_cleavage_sitec

five_prime_RSTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001469

has super-classes
RSTc

five_prime_sticky_end_restriction_enzyme_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001975

Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
has super-classes
sticky_end_restriction_enzyme_cleavage_sitec

five_prime_terminal_inverted_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000420

has super-classes
terminal_inverted_repeatc

five_prime_three_prime_overlapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000073

has super-classes
overlappingc

five_prime_USTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001466

has super-classes
USTc

five_prime_UTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000204

has super-classes
UTRc

five_prime_UTR_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000447

has super-classes
UTR_intronc

five_prime_UTR_premature_start_codon_location_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001990

has super-classes
5_prime_UTR_premature_start_codon_variantc

five_taurinomethyl_two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001379

has super-classes
modified_uridinec

five_taurinomethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001378

has super-classes
modified_uridinec

five_two_prime_O_dimethylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001287

has super-classes
modified_cytidinec

five_two_prime_O_dimethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001346

has super-classes
modified_uridinec

fixed_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001768

has super-classes
variant_frequencyc

flankedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000357

has super-classes
feature_attributec
has sub-classes
FRT_flankedc, floxedc

flanking_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000239

has super-classes
topologically_defined_regionc
has sub-classes
five_prime_flanking_regionc, three_prime_flanking_regionc, transposable_element_flanking_regionc

flanking_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002192

has super-classes
repeat_regionc

flanking_three_prime_quadruplet_recoding_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001281

has super-classes
three_prime_recoding_sitec

FLEX_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001846

has super-classes
promoter_elementc

floxedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000359

has super-classes
flankedc

floxed_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000363

is equivalent to
transgenec and (has_qualityop some floxedc)
has super-classes
transgenec
has_qualityop some floxedc

foldback_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000238

has super-classes
DNA_transposonc

foreignc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000784

has super-classes
feature_attributec

foreign_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000285

is equivalent to
genec and (has_qualityop some foreignc)
has super-classes
genec
has_qualityop some foreignc
has sub-classes
engineered_foreign_genec

foreign_transposable_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000720

requested by Michael on 19 Nov 2004.
is equivalent to
transposable_elementc and (has_qualityop some foreignc)
has super-classes
transposable_elementc
has_qualityop some foreignc
has sub-classes
engineered_foreign_transposable_elementc

forkhead_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001847

has super-classes
promoter_elementc

forwardc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001030

has super-classes
direction_attributec

forward_primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000121

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is equivalent to
primerc and (has_qualityop some forwardc)
has super-classes
primerc
has_qualityop some forwardc

fosmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000158

Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
has super-classes
vector_repliconc

fosmid_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000763

four_bp_start_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001269

has super-classes
non_canonical_start_codonc

four_cutter_restriction_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000244

four_demethylwyosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001341

has super-classes
modified_guanosinec

four_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001350

has super-classes
modified_uridinec

fragment_assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001249

has super-classes
assemblyc
has sub-classes
RH_mapc, STS_mapc, fingerprint_mapc

fragmentaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000731

Term added because of request by MO people.
has super-classes
statusc

frame_restoring_sequence_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000110

frame_restoring_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001591

has super-classes
frameshift_variantc

frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000865

has super-classes
mRNA_attributec
has sub-classes
minus_1_frameshiftc, minus_2_frameshiftc, plus_1_frameshiftc, plus_2_framshiftc

frameshift_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001909

has super-classes
frameshift_variantc
internal_feature_elongationc

frameshift_sequence_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000065

frameshift_truncationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001910

has super-classes
frameshift_variantc
feature_truncationc

frameshift_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001589

EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
has super-classes
protein_altering_variantc
has sub-classes
frame_restoring_variantc, frameshift_elongationc, frameshift_truncationc, frameshift_variant_NMD_escapingc, frameshift_variant_NMD_triggeringc, minus_1_frameshift_variantc, minus_2_frameshift_variantc, plus_1_frameshift_variantc, plus_2_frameshift_variantc

frameshift_variant_NMD_escapingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002324

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
frameshift_variantc
NMD_escaping_variantc

frameshift_variant_NMD_triggeringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002323

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
frameshift_variantc
NMD_triggering_variantc

FREc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002046

Requested by Rama, SGD.
has super-classes
enhancer_binding_sitec

freec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001516

has super-classes
duplication_attributec

free_chromosome_armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000065

has super-classes
chromosome_structure_variationc

free_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000144

has super-classes
chromosomal_duplicationc
has sub-classes
free_ring_duplicationc

free_ring_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000145

is equivalent to
ring_chromosomec and (has_qualityop some freec)
has super-classes
ring_chromosomec
free_duplicationc
has_qualityop some freec

FRT_flankedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000361

has super-classes
flankedc

FRT_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000350

has super-classes
inversion_sitec

function_uncertain_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002220

Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019.
has super-classes
functional_effect_variantc

functional_candidate_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001869

Requested by Bayer Cropscience December, 2011.
has super-classes
candidate_genec

functional_effect_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001536

Updated after request from Lea Starita, lea.starita@gmail.com from the NCBI.
has super-classes
sequence_variantc
has sub-classes
altered_gene_product_levelc, altered_gene_product_structurec, function_uncertain_variantc, functionally_abnormalc, functionally_normalc

functional_gene_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002188

A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors.
has super-classes
gene_member_regionc

functionally_abnormalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002218

Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019.
has super-classes
functional_effect_variantc
has sub-classes
NMD_escaping_variantc, NMD_triggering_variantc, dominant_negative_variantc, gain_of_function_variantc, lethal_variantc, loss_of_function_variantc, loss_of_heterozygosityc, null_mutationc, transcript_function_variantc, translational_product_function_variantc

functionally_normalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002219

Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019.
has super-classes
functional_effect_variantc

fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000806

has super-classes
feature_attributec

fusion_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000287

is equivalent to
genec and (has_qualityop some fusionc)
has super-classes
genec
has_qualityop some fusionc
has sub-classes
engineered_fusion_genec

G_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001980

A plant specific region.
has super-classes
regulatory_promoter_elementc

G_quartetc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000003

has super-classes
sequence_secondary_structurec

G_to_A_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000016

has super-classes
purine_transitionc

G_to_C_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000026

has super-classes
purine_to_pyrimidine_transversionc

G_to_T_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000027

has super-classes
purine_to_pyrimidine_transversionc

GAGA_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001166

has super-classes
DNA_motifc
part_ofop some RNApol_II_promoterc

gain_of_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002053

has super-classes
functionally_abnormalc

galactosyl_queuosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001319

has super-classes
seven_deazaguanosinec

gamma_turnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001138

has super-classes
polypeptide_turn_motifc
has sub-classes
gamma_turn_classicc, gamma_turn_inversec

gamma_turn_classicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001139

has super-classes
gamma_turnc

gamma_turn_inversec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001140

has super-classes
gamma_turnc

gapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000730

has super-classes
assembly_componentc
part_ofop some sequence_assemblyc

GATA_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001840

Changed to is_a SO:0001055 transcriptional_cis_regulatory_region from core_eukaryotic_promoter_element SO:0001660 after Ruth Lovering from GREEKC initiative pointed out that GATA boxes are frequently in enhancer regions, Dave Sant Aug 2020. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.
has super-classes
TF_binding_sitec
has sub-classes
iron_repressed_GATA_elementc

GC_rich_promoter_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000173

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

GcvB_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000379

has super-classes
DsrA_RNAc

genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000704

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
has super-classes
biological_regionc
member_ofop some gene_groupc
has sub-classes
candidate_genec, cryptic_genec, engineered_genec, epigenetically_modified_genec, foreign_genec, fusion_genec, gene_cassettec, gene_with_non_canonical_start_codonc, gene_with_polycistronic_transcriptc, gene_with_trans_spliced_transcriptc, mt_genec, ncRNA_genec, negatively_autoregulated_genec, nuclear_genec, nucleomorph_genec, plasmid_genec, plastid_genec, positively_autoregulated_genec, post_translationally_regulated_genec, predicted_genec, protein_coding_genec, proviral_genec, recombinationally_rearranged_genec, rescue_genec, retrogenec, silenced_genec, transgenec, translationally_regulated_genec, transposable_element_genec, vertebrate_immune_system_genec

gene_arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005851

This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
has super-classes
gene_groupc

gene_array_memberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000081

has super-classes
gene_attributec
has sub-classes
gene_cassette_memberc, gene_subarray_memberc, member_of_regulonc, operon_memberc

gene_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000401

has super-classes
feature_attributec
has sub-classes
encodes_alternate_transcription_start_sitesc, encodes_alternately_spliced_transcriptsc, epigenetically_modifiedc, gene_array_memberc, gene_to_gene_featurec, non_protein_codingc, protein_codingc, regulatedc

gene_by_genome_locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000085

gene_by_organelle_of_genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000086

gene_by_polyadenylation_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000066

gene_by_transcript_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000064

This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.

gene_cassettec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005853

This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
has super-classes
genec

gene_cassette_arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005854

This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
has super-classes
gene_groupc
has_partop some gene_cassettec
has sub-classes
silent_mating_type_cassette_arrayc

gene_cassette_memberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005848

has super-classes
gene_array_memberc
has sub-classes
cassette_array_memberc

gene_classc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000009

gene_component_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000842

has super-classes
biological_regionc
part_ofop some genec
has sub-classes
gene_fragmentc, gene_segmentc, intein_encoding_regionc, non_transcribed_regionc, promoterc

gene_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000997

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is equivalent to
gene_component_regionc and (has_qualityop some fragmentaryc)
has super-classes
gene_component_regionc
has_qualityop some fragmentaryc

gene_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001565

has super-classes
gene_variantc
feature_fusionc
has sub-classes
bidirectional_gene_fusionc, unidirectional_gene_fusionc

gene_groupc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005855

has super-classes
biological_regionc
has sub-classes
gene_arrayc, gene_cassette_arrayc, gene_subarrayc, mating_type_regionc, operonc, regulonc

gene_group_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000752

Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529.

gene_member_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000831

A manufactured term used to allow the parts of a gene to have an is_a path to the root.
has super-classes
biological_regionc
member_ofop some genec
has sub-classes
functional_gene_regionc, regulatory_regionc, transcriptc

gene_not_polyadenylatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000438

gene_partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000050

gene_rearranged_at_DNA_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000138

is equivalent to
epigenetically_modified_genec and (has_qualityop some rearranged_at_DNA_levelc)
has super-classes
epigenetically_modified_genec
has_qualityop some rearranged_at_DNA_levelc

gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_3000000

Requested by tracker 2021594, July 2008, by Alex.
has super-classes
gene_component_regionc
has sub-classes
pseudogenic_gene_segmentc

gene_sensu_your_favorite_organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000008

gene_silenced_by_DNA_methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000129

is equivalent to
gene_silenced_by_DNA_modificationc and (has_qualityop some silenced_by_DNA_methylationc)
has super-classes
gene_silenced_by_DNA_modificationc
has_qualityop some silenced_by_DNA_methylationc

gene_silenced_by_DNA_modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000128

is equivalent to
genec and (has_qualityop some silenced_by_DNA_modificationc)
has super-classes
silenced_genec
has_qualityop some silenced_by_DNA_modificationc
has sub-classes
gene_silenced_by_DNA_methylationc

gene_silenced_by_histone_deacetylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001227

is equivalent to
gene_silenced_by_histone_modificationc and (has_qualityop some silenced_by_histone_deacetylationc)
has super-classes
gene_silenced_by_histone_modificationc
has_qualityop some silenced_by_histone_deacetylationc

gene_silenced_by_histone_methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001226

is equivalent to
gene_silenced_by_histone_modificationc and (has_qualityop some silenced_by_histone_methylationc)
has super-classes
gene_silenced_by_histone_modificationc
has_qualityop some silenced_by_histone_methylationc

gene_silenced_by_histone_modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001225

is equivalent to
silenced_genec and (has_qualityop some silenced_by_histone_modificationc)
has super-classes
silenced_genec
has_qualityop some silenced_by_histone_modificationc
has sub-classes
gene_silenced_by_histone_deacetylationc, gene_silenced_by_histone_methylationc

gene_silenced_by_RNA_interferencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001224

is equivalent to
silenced_genec and (has_qualityop some silenced_by_RNA_interferencec)
has super-classes
silenced_genec
has_qualityop some silenced_by_RNA_interferencec

gene_subarrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005852

This would include, for example, a cluster of genes encoding different histones.
has super-classes
gene_groupc

gene_subarray_memberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005849

has super-classes
gene_array_memberc

gene_to_gene_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000067

has super-classes
gene_attributec
has sub-classes
overlappingc

gene_trap_constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001477

has super-classes
engineered_plasmidc

gene_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001564

has super-classes
feature_variantc
has sub-classes
gene_fusionc, genic_downstream_transcript_variantc, genic_upstream_transcript_variantc, transcript_variantc, translational_product_structure_variantc

gene_with_dicistronic_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000722

Requested by MA nov 19 2004.
is equivalent to
gene_with_dicistronic_transcriptc and (transcribed_toop some dicistronic_mRNAc)
has super-classes
gene_with_dicistronic_transcriptc
transcribed_toop some dicistronic_mRNAc

gene_with_dicistronic_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000721

Requested by Michael, 19 nov 2004.
is equivalent to
gene_with_dicistronic_transcriptc and (transcribed_toop some dicistronic_primary_transcriptc)
has super-classes
gene_with_dicistronic_transcriptc
transcribed_toop some dicistronic_primary_transcriptc

gene_with_dicistronic_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000692

is equivalent to
gene_with_polycistronic_transcriptc and (transcribed_toop some dicistronic_transcriptc)
has super-classes
gene_with_polycistronic_transcriptc
transcribed_toop some dicistronic_transcriptc
has sub-classes
gene_with_dicistronic_mRNAc, gene_with_dicistronic_primary_transcriptc

gene_with_edited_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000548

is equivalent to
protein_coding_genec and (transcribed_toop some edited_transcriptc)
has super-classes
protein_coding_genec
transcribed_toop some edited_transcriptc

gene_with_mRNA_recoded_by_translational_bypassc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000711

is equivalent to
protein_coding_genec and (has_qualityop some recoded_by_translational_bypassc)
has super-classes
gene_with_recoded_mRNAc
has_qualityop some recoded_by_translational_bypassc

gene_with_mRNA_with_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000455

is equivalent to
protein_coding_genec and (has_qualityop some frameshiftc)
has super-classes
protein_coding_genec
has_qualityop some frameshiftc

gene_with_non_canonical_start_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001739

Requested by flybase, Dec 2010.
is equivalent to
genec and (containsop some non_canonical_start_codonc)
has super-classes
genec
containsop some non_canonical_start_codonc
has sub-classes
gene_with_start_codon_CUGc

gene_with_polyadenylated_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000451

is equivalent to
protein_coding_genec and (transcribed_toop some polyadenylated_mRNAc)
has super-classes
protein_coding_genec
transcribed_toop some polyadenylated_mRNAc

gene_with_polycistronic_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000690

is equivalent to
genec and (transcribed_toop some polycistronic_transcriptc)
has super-classes
genec
transcribed_toop some polycistronic_transcriptc
has sub-classes
gene_with_dicistronic_transcriptc

gene_with_recoded_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000693

is equivalent to
protein_coding_genec and (has_qualityop some recodedc)
has super-classes
protein_coding_genec
has_qualityop some recodedc
has sub-classes
gene_with_mRNA_recoded_by_translational_bypassc, gene_with_stop_codon_read_throughc, gene_with_transcript_with_translational_frameshiftc

gene_with_start_codon_CUGc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001740

Requested by flybase, Dec 2010.
has super-classes
gene_with_non_canonical_start_codonc

gene_with_stop_codon_read_throughc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000697

is equivalent to
gene_with_recoded_mRNAc and (has_partop some stop_codon_read_throughc)
has super-classes
gene_with_recoded_mRNAc
has_partop some stop_codon_read_throughc
has sub-classes
gene_with_stop_codon_redefined_as_pyrrolysinec, gene_with_stop_codon_redefined_as_selenocysteinec

gene_with_stop_codon_redefined_as_pyrrolysinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000698

is equivalent to
gene_with_recoded_mRNAc and (has_partop some stop_codon_redefined_as_pyrrolysinec)
has super-classes
gene_with_stop_codon_read_throughc
has_partop some stop_codon_redefined_as_pyrrolysinec

gene_with_stop_codon_redefined_as_selenocysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000710

is equivalent to
gene_with_stop_codon_read_throughc and (has_partop some stop_codon_redefined_as_selenocysteinec)
has super-classes
gene_with_stop_codon_read_throughc
has_partop some stop_codon_redefined_as_selenocysteinec

gene_with_trans_spliced_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000459

is equivalent to
genec and (transcribed_toop some trans_spliced_transcriptc)
has super-classes
genec
transcribed_toop some trans_spliced_transcriptc

gene_with_transcript_with_translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000712

is equivalent to
gene_with_recoded_mRNAc and (has_qualityop some translationally_frameshiftedc)
has super-classes
gene_with_recoded_mRNAc
has_qualityop some translationally_frameshiftedc

genetic_markerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001645

has super-classes
biological_regionc
has sub-classes
DArT_markerc, heritable_phenotypic_markerc, selection_markerc

genic_downstream_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002152

has super-classes
gene_variantc

genic_upstream_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002153

has super-classes
gene_variantc

genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001026

is equivalent to
sequence_collectionc and (has_partop some repliconc)
has super-classes
sequence_collectionc
has_partop some repliconc
has sub-classes
kinetoplastc, reference_genomec, variant_genomec

genomic_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000040

is equivalent to
clonec and (has_qualityop some genomic_DNAc)
has super-classes
clonec
has_qualityop some genomic_DNAc

genomic_DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000991

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
DNAc

genomic_DNA_contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002209

Requested by Bayer Crop Science, March 2018
has super-classes
contigc

genomic_DNA_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001828

has super-classes
readc

genomic_islandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000772

Genomic islands are transmissible elements characterized by large size (>10kb).
has super-classes
integrated_mobile_genetic_elementc
has sub-classes
adaptive_islandc, cryptic_prophagec, defective_conjugative_transposonc, metabolic_islandc, pathogenic_islandc, symbiosis_islandc

genomically_contaminated_cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000811

is equivalent to
invalidated_cDNA_clonec and (has_qualityop some invalidated_by_genomic_contaminationc)
has super-classes
invalidated_cDNA_clonec
has_qualityop some invalidated_by_genomic_contaminationc

genomically_imprintedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000134

has super-classes
regulatedc
epigenetically_modifiedc
has sub-classes
maternally_imprintedc, paternally_imprintedc

genotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001027

has super-classes
variant_collectionc
variant_ofop some genomec

germline_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001778

has super-classes
variant_originc

glutamic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001454

A place holder for a cross product with chebi.
has super-classes
amino_acidc

glutamic_acid_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000216

has super-classes
tRNA_primary_transcriptc

glutaminec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001448

A place holder for a cross product with chebi.
has super-classes
amino_acidc

glutamine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000217

has super-classes
tRNA_primary_transcriptc

glutaminyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000259

has super-classes
tRNAc
derives_fromop some glutamic_acid_tRNA_primary_transcriptc

glutamyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000260

has super-classes
tRNAc
derives_fromop some glutamine_tRNA_primary_transcriptc

glycinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001443

A place holder for a cross product with chebi.
has super-classes
amino_acidc

glycine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000218

has super-classes
tRNA_primary_transcriptc

glycyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000261

has super-classes
tRNAc
derives_fromop some glycine_tRNA_primary_transcriptc

GNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001192

Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
has super-classes
nucleic_acidc
has sub-classes
R_GNAc, S_GNAc

GNA_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001193

is equivalent to
synthetic_oligoc and (has_qualityop some GNAc)
has super-classes
synthetic_oligoc
has_qualityop some GNAc
has sub-classes
R_GNA_oligoc, S_GNA_oligoc

golden_pathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000688

has super-classes
sequence_assemblyc

golden_path_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000468

has super-classes
assembly_componentc
part_ofop some golden_pathc

gRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000979

has super-classes
non_protein_codingc

gRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001264

is equivalent to
ncRNA_genec and (has_qualityop some gRNA_encodingc)
has super-classes
ncRNA_genec
has_qualityop some gRNA_encodingc

group_1_intron_homing_endonuclease_target_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000354

has super-classes
nuclease_sensitive_sitec

group_I_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000587

GO:0000372.
has super-classes
autocatalytically_spliced_intronc

group_II_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000603

GO:0000373.
has super-classes
autocatalytically_spliced_intronc
has sub-classes
group_IIA_intronc, group_IIB_intronc, group_IIC_intronc

group_IIA_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000381

has super-classes
group_II_intronc

group_IIB_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000382

has super-classes
group_II_intronc

group_IIC_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002226

has super-classes
group_II_intronc

group_III_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001213

GO:0000374.
has super-classes
autocatalytically_spliced_intronc

GT_dinucleotide_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001862

paper:PMID:16043634.
has super-classes
dinucleotide_repeat_microsatellite_featurec

GTT_trinucleotide_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001863

has super-classes
trinucleotide_repeat_microsatellite_featurec

guide_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000602

has super-classes
ncRNAc

guide_RNA_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000930

has super-classes
mature_transcript_regionc
part_ofop some guide_RNAc
has sub-classes
anchor_regionc, template_regionc

Gypsy_LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002265

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LTR_retrotransposonc

H2AK5_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001938

has super-classes
histone_2A_acetylation_sitec

H2AK9_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001944

has super-classes
histone_2A_acetylation_sitec

H2AZK11_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002147

has super-classes
histone_2AZ_acetylation_sitec

H2AZK13_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002148

has super-classes
histone_2AZ_acetylation_sitec

H2AZK15_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002149

has super-classes
histone_2AZ_acetylation_sitec

H2AZK4_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002145

has super-classes
histone_2AZ_acetylation_sitec

H2AZK7_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002146

has super-classes
histone_2AZ_acetylation_sitec

H2B_ubiquitination_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001717

has super-classes
histone_ubiqitination_sitec

H2BK120_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001940

has super-classes
histone_2B_acetylation_sitec

H2BK12_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001937

has super-classes
histone_2B_acetylation_sitec

H2BK15_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001946

has super-classes
histone_2B_acetylation_sitec

H2BK20_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001942

has super-classes
histone_2B_acetylation_sitec

H2BK5_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002164

has super-classes
histone_2B_acetylation_sitec

H2BK5_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001714

has super-classes
histone_methylation_sitec

H3K14_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001704

has super-classes
histone_3_acetylation_sitec

H3K18_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001718

has super-classes
histone_3_acetylation_sitec

H3K20_trimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001935

has super-classes
histone_methylation_sitec

H3K23_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001719

has super-classes
histone_3_acetylation_sitec

H3K23_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001951

has super-classes
histone_methylation_sitec

H3K27_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002049

Requested by: Sagar Jain, Richard Scheuermann.
has super-classes
histone_3_acetylation_sitec

H3K27_acylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001721

H3K27_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001726

has super-classes
H3K27_methylation_sitec

H3K27_methylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001732

has super-classes
histone_methylation_sitec
has sub-classes
H3K27_dimethylation_sitec, H3K27_monomethylation_sitec, H3K27_trimethylation_sitec

H3K27_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001708

has super-classes
H3K27_methylation_sitec

H3K27_trimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001709

has super-classes
H3K27_methylation_sitec

H3K36_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001936

has super-classes
histone_3_acetylation_sitec

H3K36_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001723

has super-classes
H3K36_methylation_sitec

H3K36_methylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001733

has super-classes
histone_methylation_sitec
has sub-classes
H3K36_dimethylation_sitec, H3K36_monomethylation_sitec, H3K36_trimethylation_sitec

H3K36_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001722

has super-classes
H3K36_methylation_sitec

H3K36_trimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001724

has super-classes
H3K36_methylation_sitec

H3K4_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001943

has super-classes
histone_3_acetylation_sitec

H3K4_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001725

has super-classes
H3K4_methylation_sitec

H3K4_methylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001734

has super-classes
histone_methylation_sitec
has sub-classes
H3K4_dimethylation_sitec, H3K4_monomethylation_sitec, H3K4_trimethylationc

H3K4_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001705

has super-classes
H3K4_methylation_sitec

H3K4_trimethylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001706

has super-classes
H3K4_methylation_sitec

H3K56_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001945

has super-classes
histone_3_acetylation_sitec

H3K79_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001711

has super-classes
H3K79_methylation_sitec

H3K79_methylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001735

has super-classes
histone_methylation_sitec
has sub-classes
H3K79_dimethylation_sitec, H3K79_monomethylation_sitec, H3K79_trimethylation_sitec

H3K79_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001710

has super-classes
H3K79_methylation_sitec

H3K79_trimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001712

has super-classes
H3K79_methylation_sitec

H3K9_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001703

has super-classes
histone_3_acetylation_sitec

H3K9_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001728

has super-classes
H3K9_methylation_sitec

H3K9_methylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001736

has super-classes
histone_methylation_sitec
has sub-classes
H3K9_dimethylation_sitec, H3K9_monomethylation_sitec, H3K9_trimethylation_sitec

H3K9_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001727

has super-classes
H3K9_methylation_sitec

H3K9_trimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001707

has super-classes
H3K9_methylation_sitec

H3R2_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001948

has super-classes
histone_methylation_sitec

H3R2_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001947

has super-classes
histone_methylation_sitec

H4K12_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001939

has super-classes
histone_4_acetylation_sitec

H4K16_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001729

has super-classes
histone_4_acetylation_sitec

H4K20_monomethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001713

has super-classes
histone_methylation_sitec

H4K4_trimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001950

has super-classes
histone_methylation_sitec

H4K5_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001730

has super-classes
histone_4_acetylation_sitec

H4K8_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001731

has super-classes
histone_4_acetylation_sitec

H4K91_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001941

has super-classes
histone_4_acetylation_sitec

H4K_acylation_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001738

has super-classes
histone_acylation_regionc

H4R3_dimethylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001949

has super-classes
histone_methylation_sitec

H_ACA_box_snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000594

has super-classes
snoRNAc
derives_fromop some H_ACA_box_snoRNA_primary_transcriptc
has sub-classes
pseudouridylation_guide_snoRNAc

H_ACA_box_snoRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000608

has super-classes
snoRNA_encodingc

H_ACA_box_snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000596

has super-classes
snoRNA_primary_transcriptc

H_pseudoknotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000592

has super-classes
pseudoknotc

hammerhead_ribozymec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000380

is equivalent to
RNA_motifc and (has_qualityop some ribozymicc)
has super-classes
RNA_motifc
has_qualityop some ribozymicc

haplotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001024

has super-classes
variant_collectionc
variant_ofop some haplotype_blockc

haplotype_blockc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000355

has super-classes
recombination_featurec

hAT_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002279

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

helitronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000544

has super-classes
DNA_transposonc

helix_turn_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001081

has super-classes
polypeptide_structural_motifc
has_partop some peptide_helixc
has_partop some polypeptide_turn_motifc

heptamer_of_recombination_feature_of_vertebrate_immune_system_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000561

has super-classes
vertebrate_immune_system_gene_recombination_signal_featurec
has sub-classes
J_heptamerc, V_heptamerc, five_prime_D_heptamerc, three_prime_D_heptamerc

heritable_phenotypic_markerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001500

has super-classes
genetic_markerc

HERV_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002067

has super-classes
mobile_element_deletionc
derives_fromop some Endogenous_Retrovirus_LTR_retrotransposonc

HERV_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002187

has super-classes
mobile_element_insertionc
derives_fromop some Endogenous_Retrovirus_LTR_retrotransposonc

hetero_compound_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000140

has super-classes
compound_chromosomec

high_identity_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001502

Requested by tracker ID: 2902685.
has super-classes
experimental_featurec

high_quality_draftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001487

has super-classes
whole_genome_sequence_statusc

histidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001452

A place holder for a cross product with chebi.
has super-classes
amino_acidc

histidine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000219

has super-classes
tRNA_primary_transcriptc

histidyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000262

has super-classes
tRNAc
derives_fromop some histidine_tRNA_primary_transcriptc

histone_2A_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002142

has super-classes
histone_acetylation_sitec
has sub-classes
H2AK5_acetylation_sitec, H2AK9_acetylation_sitec, histone_2AZ_acetylation_sitec

histone_2AZ_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002144

has super-classes
histone_2A_acetylation_sitec
has sub-classes
H2AZK11_acetylation_sitec, H2AZK13_acetylation_sitec, H2AZK15_acetylation_sitec, H2AZK4_acetylation_sitec, H2AZK7_acetylation_sitec

histone_2B_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002143

has super-classes
histone_acetylation_sitec
has sub-classes
H2BK120_acetylation_sitec, H2BK12_acetylation_sitec, H2BK15_acetylation_sitec, H2BK20_acetylation_sitec, H2BK5_acetylation_sitec

histone_3_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001973

has super-classes
histone_acetylation_sitec
has sub-classes
H3K14_acetylation_sitec, H3K18_acetylation_sitec, H3K23_acetylation_sitec, H3K27_acetylation_sitec, H3K36_acetylation_sitec, H3K4_acetylation_sitec, H3K56_acetylation_sitec, H3K9_acetylation_sitec

histone_4_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001972

has super-classes
histone_acetylation_sitec
has sub-classes
H4K12_acetylation_sitec, H4K16_acetylation_sitec, H4K5_acetylation_sitec, H4K8_acetylation_sitec, H4K91_acetylation_sitec

histone_acetylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001702

has super-classes
histone_modificationc
has sub-classes
histone_2A_acetylation_sitec, histone_2B_acetylation_sitec, histone_3_acetylation_sitec, histone_4_acetylation_sitec

histone_acylation_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001737

has super-classes
histone_modificationc
has sub-classes
H4K_acylation_regionc

histone_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001383

has super-classes
nucleotide_to_protein_binding_sitec

histone_methylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001701

has super-classes
histone_modificationc
has sub-classes
H2BK5_monomethylation_sitec, H3K20_trimethylation_sitec, H3K23_dimethylation_sitec, H3K27_methylation_sitec, H3K36_methylation_sitec, H3K4_methylation_sitec, H3K79_methylation_sitec, H3K9_methylation_sitec, H3R2_dimethylation_sitec, H3R2_monomethylation_sitec, H4K20_monomethylation_sitec, H4K4_trimethylation_sitec, H4R3_dimethylation_sitec

histone_modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001700

is equivalent to
post_translationally_modified_regionc and (has_qualityop some epigenetically_modifiedc)
has super-classes
post_translationally_modified_regionc
epigenetically_modified_regionc
has_qualityop some epigenetically_modifiedc
has sub-classes
histone_acetylation_sitec, histone_acylation_regionc, histone_methylation_sitec, histone_ubiqitination_sitec

histone_ubiqitination_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001716

has super-classes
histone_modificationc
has sub-classes
H2B_ubiquitination_sitec

homing_endonuclease_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001257

has super-classes
nuclease_binding_sitec

homo_compound_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000138

has super-classes
compound_chromosomec

homol_D_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001848

has super-classes
core_eukaryotic_promoter_elementc

homol_E_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001849

has super-classes
promoter_elementc

homologousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000857

has super-classes
conservedc
has sub-classes
orthologousc, paralogousc

homologous_chromosome_recognition_and_pairing_locusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002233

Added as per request by Val Wood GitHub issue #483 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/483)
has super-classes
binding_sitec
member_ofop some chromosome_partc

homologous_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000853

is equivalent to
conserved_regionc and (has_qualityop some homologousc)
has super-classes
conserved_regionc
has_qualityop some homologousc
has sub-classes
orthologous_regionc, paralogous_regionc

Hoogsteen_base_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000500

has super-classes
base_pairc

HSEc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001850

has super-classes
promoter_elementc

hydrophobic_region_of_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100013

Range.
has super-classes
polypeptide_regionc

hydroxywybutosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001334

has super-classes
modified_guanosinec

hyperploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000055

has super-classes
aneuploidc

hypoploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000056

has super-classes
aneuploidc

I-boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001982

has super-classes
regulatory_promoter_elementc

I_LINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002273

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LINE_elementc

i_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001010

has super-classes
DNA_sequence_secondary_structurec

iDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000723

has super-classes
recombination_featurec

IG_C_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002123

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_genec

IG_C_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002100

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_pseudogenec

IG_D_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002124

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_genec

IG_J_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002125

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_genec

IG_J_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002101

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_pseudogenec

IG_V_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002126

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_genec

IG_V_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002102

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
immunoglobulin_pseudogenec

immature_peptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001063

Range.
has super-classes
polypeptide_regionc

immunoglobulin_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002122

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
vertebrate_immune_system_genec
has sub-classes
IG_C_genec, IG_D_genec, IG_J_genec, IG_V_genec

immunoglobulin_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002098

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
vertebrate_immune_system_pseudogenec
has sub-classes
IG_C_pseudogenec, IG_J_pseudogenec, IG_V_pseudogenec

immunoglobulin_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001832

has super-classes
polypeptide_regionc
has sub-classes
C_regionc, V_regionc

imprinting_control_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002191

Moved from is_a regulatory_region (SO:0005836) to is_a epigenetically_modified_region (SO:0001720) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530.
has super-classes
epigenetically_modified_regionc

improved_high_quality_draftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001488

has super-classes
whole_genome_sequence_statusc

inactive_catalytic_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001618

has super-classes
inactive_ligand_binding_sitec

inactive_ligand_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001560

has super-classes
polypeptide_loss_of_function_variantc
has sub-classes
inactive_catalytic_sitec

incomplete_terminal_codon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001626

EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
has super-classes
terminator_codon_variantc
inframe_variantc

incomplete_transcript_3UTR_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002076

has super-classes
incomplete_transcript_variantc

incomplete_transcript_5UTR_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002077

has super-classes
incomplete_transcript_variantc

incomplete_transcript_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002081

has super-classes
incomplete_transcript_variantc

incomplete_transcript_coding_splice_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002082

has super-classes
incomplete_transcript_splice_region_variantc

incomplete_transcript_exonic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002080

has super-classes
incomplete_transcript_variantc

incomplete_transcript_intronic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002078

has super-classes
incomplete_transcript_variantc

incomplete_transcript_splice_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002079

has super-classes
incomplete_transcript_variantc
has sub-classes
incomplete_transcript_coding_splice_variantc

incomplete_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002075

This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation. It is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems.
has super-classes
transcript_variantc
has sub-classes
incomplete_transcript_3UTR_variantc, incomplete_transcript_5UTR_variantc, incomplete_transcript_CDSc, incomplete_transcript_exonic_variantc, incomplete_transcript_intronic_variantc, incomplete_transcript_splice_region_variantc

increased_gene_product_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002315

Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
has super-classes
altered_gene_product_levelc

increased_polyadenylation_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001802

Term requested by M. Dumontier, June 1 2011.
has super-classes
polyadenylation_variantc

increased_transcript_level_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001542

has super-classes
level_of_transcript_variantc

increased_transcript_stability_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001548

has super-classes
transcript_stability_variantc

increased_transcription_rate_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001551

has super-classes
rate_of_transcription_variantc

increased_translational_product_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001556

has super-classes
translational_product_level_variantc

indel_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002173

has super-classes
sequence_alteration_artifactc

independently_knownc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000906

has super-classes
statusc

inducible_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002051

has super-classes
promoterc

inert_DNA_spacerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002223

Updated by Evan Christensen on May 27, 2021 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/494
has super-classes
regulatory_regionc

inframec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001817

has super-classes
mRNA_attributec

inframe_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001822

has super-classes
inframe_indelc
feature_truncationc
has sub-classes
conservative_inframe_deletionc, disruptive_inframe_deletionc

inframe_indelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001820

has super-classes
inframe_variantc
has sub-classes
inframe_deletionc, inframe_insertionc

inframe_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001821

has super-classes
inframe_indelc
internal_feature_elongationc
has sub-classes
conservative_inframe_insertionc, disruptive_inframe_insertionc

inframe_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001650

has super-classes
protein_altering_variantc
has sub-classes
incomplete_terminal_codon_variantc, inframe_indelc, nonsynonymous_variantc

initiator_codon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001582

This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.
has super-classes
coding_sequence_variantc
has sub-classes
start_lostc, start_retained_variantc

inosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001230

The free molecule is CHEBI:17596.
has super-classes
modified_RNA_base_featurec
has sub-classes
modified_inosinec

INR1_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001163

has super-classes
DNA_motifc
part_ofop some RNApol_II_promoterc

INR_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000014

Binds TAF1, TAF2.
has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_II_core_promoterc

insertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000046

insert_AAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000928

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_AUc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000927

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_Cc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000920

insert_CUc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000926

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_dinucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000921

insert_Gc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000923

insert_GCc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000924

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_GUc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000925

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_Uc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000917

The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.

insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000667

has super-classes
sequence_alterationc
biological_regionc
has sub-classes
duplicationc, mobile_element_insertionc, novel_sequence_insertionc, transgenic_insertionc

insertion_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002175

has super-classes
sequence_alteration_artifactc
has sub-classes
duplication_artifactc

insertion_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001512

has super-classes
alteration_attributec
has sub-classes
directc, invertedc, tandemc

insertion_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001414

has super-classes
chromosome_breakpointc

insertion_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000973

has super-classes
terminal_inverted_repeat_elementc

insertion_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000366

has super-classes
junctionc
has sub-classes
transposable_element_insertion_sitec

insertionalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001522

has super-classes
translocaton_attributec

insertional_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000154

has super-classes
chromosomal_duplicationc
has sub-classes
inverted_insertional_duplicationc, uninverted_insertional_duplicationc, unoriented_insertional_duplicationc

inside_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000069

has super-classes
overlappingc
has sub-classes
inside_intron_antiparallelc, inside_intron_parallelc

inside_intron_antiparallelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000070

has super-classes
inside_intronc

inside_intron_parallelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000071

has super-classes
inside_intronc

insulatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000627

moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
has super-classes
cis_regulatory_modulec
has sub-classes
boundary_elementc, enhancer_blocking_elementc

insulator_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001460

See tracker ID 2060908.
has super-classes
nucleotide_to_protein_binding_sitec
part_ofop some insulatorc

integrase_coding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000369

integrated_mobile_genetic_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001039

has super-classes
mobile_genetic_elementc
has sub-classes
cointegrated_plasmidc, genomic_islandc, integrated_plasmidc, integronc, proviral_regionc, transposable_elementc

integrated_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001040

is equivalent to
integrated_mobile_genetic_elementc and (derives_fromop some plasmidc)
has super-classes
integrated_mobile_genetic_elementc
derives_fromop some plasmidc

integration_excision_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000946

has super-classes
site_specific_recombination_target_regionc
has sub-classes
attB_sitec, attC_sitec, attCtn_sitec, attI_sitec, attL_sitec, attP_sitec, attR_sitec

integronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000365

has super-classes
integrated_mobile_genetic_elementc

inteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000728

Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
has super-classes
cleaved_peptide_regionc

intein_containingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000729

has super-classes
protein_codingc

intein_encoding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002026

Requested by Janos Demeter 2014.
has super-classes
gene_component_regionc

interbandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000450

has super-classes
chromosome_partc

interchromosomalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001511

has super-classes
chromosomal_variation_attributec

interchromosomal_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001873

has super-classes
chromosome_breakpointc

interchromosomal_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000457

has super-classes
chromosomal_duplicationc

interchromosomal_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000031

is equivalent to
chromosome_structure_variationc and (has_qualityop some interchromosomalc)
has super-classes
chromosome_structure_variationc
has_qualityop some interchromosomalc
has sub-classes
bipartite_duplicationc, chromosomal_translocationc, interchromosomal_transpositionc

interchromosomal_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002060

has super-classes
chromosomal_translocationc
has sub-classes
cyclic_translocationc

interchromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000155

has super-classes
chromosomal_transpositionc
interchromosomal_mutationc
has sub-classes
deficient_interchromosomal_transpositionc, inverted_interchromosomal_transpositionc, uninverted_interchromosomal_transpositionc, unoriented_interchromosomal_transpositionc

intergenic_1kb_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002074

This term is added to map to the Annovar annotation 'upstream,downstream' .
has super-classes
intergenic_variantc

intergenic_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000605

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
biological_regionc

intergenic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001628

EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
has super-classes
feature_variantc
has sub-classes
conserved_intergenic_variantc, downstream_gene_variantc, downstream_transcript_variantc, intergenic_1kb_variantc, upstream_gene_variantc, upstream_transcript_variantc

interior_coding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000004

has super-classes
coding_exonc

interior_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000201

has super-classes
exonc

interior_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000191

has super-classes
intronc

intermediatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000933

has super-classes
feature_attributec

intermediate_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001677

has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_III_promoter_type_1c

internal_eliminated_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000671

has super-classes
sequence_rearrangement_featurec

internal_feature_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001908

has super-classes
feature_elongationc
has sub-classes
frameshift_elongationc, inframe_insertionc

internal_guide_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001016

has super-classes
intron_domainc
part_ofop some group_I_intronc

internal_ribosome_entry_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000243

has super-classes
ribosome_entry_sitec
has sub-classes
internal_Shine_Dalgarno_sequencec

internal_Shine_Dalgarno_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001260

has super-classes
internal_ribosome_entry_sitec
recoding_stimulatory_regionc

internal_transcribed_spacer_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000639

has super-classes
transcribed_spacer_regionc

internal_UTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000241

has super-classes
UTRc

intrachromosomalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001510

has super-classes
chromosomal_variation_attributec

intrachromosomal_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001874

has super-classes
chromosome_breakpointc

intrachromosomal_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000038

is equivalent to
intrachromosomal_mutationc and (has_partop some duplicationc)
has super-classes
intrachromosomal_mutationc
chromosomal_duplicationc
has_partop some duplicationc
has sub-classes
bipartite_duplicationc, intrachromosomal_transpositionc, inversion_derived_bipartite_duplicationc, inversion_derived_deficiency_plus_duplicationc, inversion_derived_duplication_plus_aneuploidc

intrachromosomal_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000028

is equivalent to
chromosome_structure_variationc and (has_qualityop some intrachromosomalc)
has super-classes
chromosome_structure_variationc
has_qualityop some intrachromosomalc
has sub-classes
chromosomal_deletionc, chromosomal_inversionc, chromosome_fissionc, intrachromosomal_duplicationc, ring_chromosomec

intrachromosomal_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002061

has super-classes
chromosomal_translocationc

intrachromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000041

is equivalent to
intrachromosomal_mutationc and (has_partop some translocationc) and (has_partop some duplicationc)
has super-classes
chromosomal_transpositionc
intrachromosomal_duplicationc
has_partop some duplicationc
has_partop some translocationc
has sub-classes
deficient_intrachromosomal_transpositionc, uninverted_intrachromosomal_transpositionc, unoriented_intrachromosomal_transpositionc

intragenic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002011

Requested by Pablo Cingolani, for use in SnpEff.
has super-classes
transcript_variantc

intramembrane_polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001075

has super-classes
polypeptide_structural_regionc
part_ofop some membrane_structurec
has sub-classes
membrane_peptide_loopc, transmembrane_polypeptide_regionc

intrinsically_unstructured_polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100003

has super-classes
polypeptide_structural_regionc

introgressed_chromosome_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000664

has super-classes
chromosome_partc

intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000188

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
primary_transcript_regionc
has sub-classes
UTR_intronc, autocatalytically_spliced_intronc, endonuclease_spliced_intronc, five_prime_intronc, interior_intronc, lariat_intronc, mobile_intronc, spliceosomal_intronc, three_prime_intronc, twintronc

intron_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000661

intron_base_5c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001994

has super-classes
intron_domainc
part_ofop some extended_cis_splice_sitec

intron_domainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001014

Requested by Colin Batchelor, Feb 2007.
has super-classes
primary_transcript_regionc
part_ofop some intronc
has sub-classes
extended_intronic_splice_regionc, internal_guide_sequencec, intron_base_5c, miRtronc

intron_gain_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001573

has super-classes
splicing_variantc

intron_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001627

EBI term: Intronic variations - In intron.
has super-classes
transcript_variantc
has sub-classes
coding_transcript_intron_variantc, conserved_intron_variantc, non_coding_transcript_intron_variantc, splice_site_variantc

intronic_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001492

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc
part_ofop some intronc

intronic_splice_enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000320

has super-classes
splice_enhancerc
part_ofop some spliceosomal_intron_regionc

intronic_splicing_enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002057

intronic_splicing_silencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002056

Requested by Javier Diez Perez.
has super-classes
silencerc
part_ofop some intronc

invalidatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000790

has super-classes
statusc
has sub-classes
invalidated_by_chimeric_cDNAc, invalidated_by_genomic_contaminationc, invalidated_by_genomic_polyA_primed_cDNAc, invalidated_by_partial_processingc

invalidated_by_chimeric_cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000362

has super-classes
invalidatedc

invalidated_by_genomic_contaminationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000414

has super-classes
invalidatedc

invalidated_by_genomic_polyA_primed_cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000415

has super-classes
invalidatedc

invalidated_by_partial_processingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000416

has super-classes
invalidatedc

invalidated_cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000809

is equivalent to
cDNA_clonec and (has_qualityop some invalidatedc)
has super-classes
cDNA_clonec
has_qualityop some invalidatedc
has sub-classes
chimeric_cDNA_clonec, genomically_contaminated_cDNA_clonec, partially_processed_cDNA_clonec, polyA_primed_cDNA_clonec

inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000036

has super-classes
sequence_alterationc
biological_regionc

inversion_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001517

has super-classes
alteration_attributec
has sub-classes
paracentricc, pericentricc

inversion_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001022

has super-classes
chromosome_breakpointc

inversion_cum_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000148

has super-classes
chromosomal_inversionc
chromosomal_translocationc
has_partop some inversionc
has sub-classes
inverted_intrachromosomal_transpositionc

inversion_derived_aneuploid_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000567

has super-classes
aneuploid_chromosomec

inversion_derived_bipartite_deficiencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000461

has super-classes
chromosomal_deletionc

inversion_derived_bipartite_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000547

has super-classes
intrachromosomal_duplicationc

inversion_derived_deficiency_plus_aneuploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000512

has super-classes
chromosomal_deletionc

inversion_derived_deficiency_plus_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000465

has super-classes
chromosomal_deletionc
intrachromosomal_duplicationc

inversion_derived_duplication_plus_aneuploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000549

has super-classes
intrachromosomal_duplicationc

inversion_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000948

A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
has super-classes
site_specific_recombination_target_regionc
has sub-classes
FRT_sitec

inversion_site_partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001048

A term created to allow the parts of an inversion site have an is_a path back to the root.
has super-classes
site_specific_recombination_target_regionc
has sub-classes
IRLinv_sitec, IRRinv_sitec

invertc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000047

invertedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001515

has super-classes
insertion_attributec

inverted_insertional_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000153

has super-classes
insertional_duplicationc

inverted_interchromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000156

has super-classes
interchromosomal_transpositionc

inverted_intrachromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000158

has super-classes
inversion_cum_translocationc
has_partop some inversionc

inverted_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000294

has super-classes
repeat_regionc
has sub-classes
terminal_inverted_repeatc

inverted_ring_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000439

has super-classes
chromosomal_inversionc
ring_chromosomec

inverted_tandem_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000040

has super-classes
tandem_duplicationc

IRLinv_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001046

has super-classes
inversion_site_partc
part_ofop some inversion_sitec

iron_repressed_GATA_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001851

The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
has super-classes
GATA_boxc

iron_responsive_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001182

has super-classes
UTR_regionc
part_ofop some UTRc

IRRinv_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001047

has super-classes
inversion_site_partc
part_ofop some inversion_sitec

isoleucinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001438

A place holder for a cross product with chebi.
has super-classes
amino_acidc

isoleucine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000220

has super-classes
tRNA_primary_transcriptc

isoleucyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000263

has super-classes
tRNAc
derives_fromop some isoleucine_tRNA_primary_transcriptc

isomiRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002167

has super-classes
miRNAc

isowyosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001342

has super-classes
modified_guanosinec

ISREc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001715

Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.
has super-classes
TF_binding_sitec

J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000511

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some C_gene_segmentc
has_partop some J_gene_segmentc

J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000513

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some J_gene_segmentc

J_gene_recombination_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000302

has super-classes
vertebrate_immune_system_gene_recombination_signal_featurec

J_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000470

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_segmentc

J_heptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000515

has super-classes
heptamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some J_gene_recombination_featurec

J_nonamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000514

has super-classes
nonamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some J_gene_recombination_featurec

J_spacerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000517

has super-classes
vertebrate_immune_system_gene_recombination_spacerc
part_ofop some J_gene_recombination_featurec

Jockey_LINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002271

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LINE_elementc

junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000699

A junction is a boundary between regions. A boundary has an extent of zero.
has super-classes
sequence_featurec
has sub-classes
chromosome_breakpointc, clone_insert_endc, clone_insert_startc, deletion_junctionc, exon_junctionc, insertion_sitec, nucleotide_cleavage_sitec, polyA_sitec, splice_junctionc, topologically_associated_domain_boundaryc, trans_splice_junctionc

K_turn_RNA_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000023

has super-classes
asymmetric_RNA_internal_loopc

KEN_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001807

has super-classes
polypeptide_conserved_motifc

kinetoplastc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000741

is equivalent to
sequence_collectionc and (has_partop some maxicirclec) and (has_partop some minicirclec)
has super-classes
genomec
has_partop some maxicirclec
has_partop some minicirclec

kinetoplast_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000089

is equivalent to
mt_genec and (has_originop some kinetoplastc)
has super-classes
mt_genec
has_originop some kinetoplastc
has sub-classes
maxicircle_genec, minicircle_genec

knobc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002257

Added as per request from GitHub Issue #487 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/487)
has super-classes
repeat_regionc

kozak_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001647

has super-classes
ribosome_entry_sitec

L1_LINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002272

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LINE_elementc

L_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001981

has super-classes
regulatory_promoter_elementc

laevosynaptic_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000143

has super-classes
autosynaptic_chromosomec

lambda_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000160

lambda_vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000754

has super-classes
vector_repliconc

LARDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002260

Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429)
has super-classes
LTR_retrotransposonc

lariat_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001958

Requested by PomBase 3604508.
has super-classes
intronc

late_origin_of_replicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002141

has super-classes
origin_of_replicationc

left_handed_peptide_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001115

has super-classes
peptide_helixc

lethal_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001773

has super-classes
functionally_abnormalc

leucinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001437

A place holder for a cross product with chebi.
has super-classes
amino_acidc

leucine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000221

has super-classes
tRNA_primary_transcriptc

leucoplast_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000823

is equivalent to
chromosomec and (has_originop some leucoplast_sequencec)
has super-classes
chromosomec
has_originop some leucoplast_sequencec

leucoplast_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000095

is equivalent to
plastid_genec and (has_originop some leucoplast_sequencec)
has super-classes
plastid_genec
has_originop some leucoplast_sequencec

leucoplast_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000747

has super-classes
plastid_sequencec

leucyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000264

has super-classes
tRNAc
derives_fromop some leucine_tRNA_primary_transcriptc

level_of_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001540

has super-classes
transcript_function_variantc
has sub-classes
decreased_transcript_level_variantc, increased_transcript_level_variantc

ligand_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001657

has super-classes
binding_sitec
has sub-classes
polypeptide_ligand_contactc

ligation_based_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001425

An example of this kind of read is one produced by ABI SOLiD.
has super-classes
readc

lincRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001463

has super-classes
lncRNAc

lincRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001641

has super-classes
lncRNA_genec

LINE1_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002069

has super-classes
mobile_element_deletionc
derives_fromop some L1_LINE_retrotransposonc

LINE1_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002064

has super-classes
mobile_element_insertionc
derives_fromop some L1_LINE_retrotransposonc

LINE_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000194

has super-classes
non_LTR_retrotransposonc
has sub-classes
I_LINE_retrotransposonc, Jockey_LINE_retrotransposonc, L1_LINE_retrotransposonc, R2_LINE_retrotransposonc, RTE_LINE_retrotransposonc

linearc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000987

Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
has super-classes
topology_attributec
is disjoint with
circularc

linear_double_stranded_DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000957

is equivalent to
double_stranded_DNA_chromosomec and (has_qualityop some linearc)
has super-classes
double_stranded_DNA_chromosomec
has_qualityop some linearc

linear_double_stranded_RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000964

is equivalent to
double_stranded_RNA_chromosomec and (has_qualityop some linearc)
has super-classes
double_stranded_RNA_chromosomec
has_qualityop some linearc

linear_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002212

has super-classes
plasmidc

linear_single_stranded_DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000959

is equivalent to
single_stranded_DNA_chromosomec and (has_qualityop some linearc)
has super-classes
single_stranded_DNA_chromosomec
has_qualityop some linearc

linear_single_stranded_RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000963

is equivalent to
single_stranded_RNA_chromosomec and (has_qualityop some linearc)
has super-classes
single_stranded_RNA_chromosomec
has_qualityop some linearc

linkage_groupc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000018

has super-classes
biological_regionc

lipoprotein_signal_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100009

has super-classes
cleaved_peptide_regionc

LNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001188

Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
has super-classes
nucleic_acidc

LNA_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001189

is equivalent to
synthetic_oligoc and (has_qualityop some LNAc)
has super-classes
synthetic_oligoc
has_qualityop some LNAc

lncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001877

has super-classes
ncRNAc
has sub-classes
antisense_lncRNAc, lincRNAc, sense_intronic_ncRNAc, sense_overlap_ncRNAc

lncRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002127

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
has super-classes
ncRNA_genec
has sub-classes
antisense_lncRNA_genec, bidirectional_promoter_lncRNAc, lincRNA_genec, sense_intronic_ncRNA_genec, sense_overlap_ncRNA_genec

lncRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002035

has super-classes
nc_primary_transcriptc
has sub-classes
lncRNA_with_retained_intronc, miR_encoding_lncRNA_primary_transcriptc

lncRNA_with_retained_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002113

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
lncRNA_primary_transcriptc

locus_control_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000037

Definition updated Nov 10 2020, Colin Logie from GREEKC helped us realize that LCRs can also be located 3' to a gene.
has super-classes
cis_regulatory_modulec

long_terminal_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000286

has super-classes
repeat_regionc
part_ofop some LTR_retrotransposonc
has sub-classes
five_prime_LTRc, solo_LTRc, three_prime_LTRc

long_terminal_repeat_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002208

has super-classes
transcriptc

loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002254

Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
has super-classes
stem_loop_regionc

loRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002033

MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do. Requested by Thomas Desvignes, Jan 2015.
has super-classes
small_regulatory_ncRNAc
part_ofop some pre_miRNAc

loss_of_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002054

has super-classes
functionally_abnormalc

loss_of_heterozygosityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001786

has super-classes
functionally_abnormalc

low_complexityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001004

has super-classes
statusc

low_complexity_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001005

is equivalent to
regionc and (has_qualityop some low_complexityc)
has super-classes
experimental_featurec
has_qualityop some low_complexityc

loxP_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000346

has super-classes
resolution_sitec

LOZ1_response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002225

Added on October 30, 2019 as per request of Val Wood request on GitHub Issue# 476 https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/476
has super-classes
zinc_repressed_elementc

LTR_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000848

has super-classes
repeat_componentc
part_ofop some long_terminal_repeatc
has sub-classes
R_LTR_regionc, U3_LTR_regionc, U5_LTR_regionc, five_prime_LTR_componentc, three_prime_LTR_componentc

LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000186

has super-classes
retrotransposonc
has sub-classes
Bel_Pao_LTR_retrotransposonc, Copia_LTR_retrotransposonc, Endogenous_Retrovirus_LTR_retrotransposonc, Gypsy_LTR_retrotransposonc, LARDc, Retrovirus_LTR_retrotransposonc, TRIMc

lysidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001289

has super-classes
modified_cytidinec

lysinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001450

A place holder for a cross product with chebi.
has super-classes
amino_acidc

lysine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000222

has super-classes
tRNA_primary_transcriptc

lysosomal_localization_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001530

has super-classes
peptide_localization_signalc

lysyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000265

has super-classes
tRNAc
derives_fromop some lysine_tRNA_primary_transcriptc

macronuclear_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000824

is equivalent to
chromosomec and (has_originop some macronuclear_sequencec)
has super-classes
chromosomec
has_originop some macronuclear_sequencec

macronuclear_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000083

has super-classes
organelle_sequencec

macronucleus_destined_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000672

has super-classes
sequence_rearrangement_featurec

major_TSSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001238

has super-classes
TSSc

mannosyl_queuosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001320

has super-classes
seven_deazaguanosinec

Mat2Pc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002157

has super-classes
silent_mating_type_cassette_arrayc

Mat3Mc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002158

has super-classes
silent_mating_type_cassette_arrayc

matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000343

has super-classes
experimental_featurec
has sub-classes
nucleotide_matchc, protein_matchc

match_partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000039

has super-classes
experimental_featurec
part_ofop some matchc

match_setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000038

maternal_uniparental_disomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001745

has super-classes
UPDc

maternal_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001775

has super-classes
variant_originc

maternally_imprintedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000135

has super-classes
genomically_imprintedc

maternally_imprinted_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000888

is equivalent to
genec and (has_qualityop some maternally_imprintedc)
has super-classes
epigenetically_modified_genec
has_qualityop some maternally_imprintedc

mathematically_defined_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001642

Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
has super-classes
experimental_featurec

mating_type_M_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001852

Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
has super-classes
promoter_elementc

mating_type_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001789

has super-classes
gene_groupc

mating_type_region_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001999

has super-classes
DNA_motifc
part_ofop some mating_type_regionc
has sub-classes
W_regionc, X_regionc, Y_regionc, Z1_regionc, Z2_regionc

mating_type_region_replication_fork_barrierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002021

Requested by Midori Harris.
has super-classes
DNA_motifc

matrix_attachment_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000036

has super-classes
chromosomal_regulatory_elementc

mature_miRNA_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001620

EBI term: Within mature miRNA - Located within a microRNA.
has super-classes
non_coding_transcript_variantc

mature_protein_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000419

This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
has super-classes
polypeptide_regionc
derives_fromop some mature_protein_region_of_CDSc
part_ofop some immature_peptide_regionc
has sub-classes
active_peptidec

mature_protein_region_of_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002249

Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
has super-classes
CDS_regionc

mature_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000233

A processed transcript cannot contain introns.
has super-classes
transcriptc
derives_fromop some primary_transcriptc
has sub-classes
mRNAc, ncRNAc

mature_transcript_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000834

A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
has super-classes
transcript_regionc
has sub-classes
guide_RNA_regionc, mRNA_regionc, tRNA_regionc, tmRNA_regionc

maxicirclec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000742

has super-classes
repliconc

maxicircle_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000654

is equivalent to
kinetoplast_genec and (part_ofop some maxicirclec)
has super-classes
kinetoplast_genec
part_ofop some maxicirclec
has sub-classes
cryptogenec

MCBc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001855

has super-classes
promoter_elementc

meiotic_recombination_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002155

has super-classes
recombination_featurec

member_of_regulonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001217

has super-classes
gene_array_memberc

membrane_peptide_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001076

has super-classes
intramembrane_polypeptide_regionc

membrane_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001071

Range.
has super-classes
polypeptide_structural_regionc

Merlin_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002281

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

metabolic_islandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000774

Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
has super-classes
genomic_islandc

metal_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001656

See GO:0046872 : metal ion binding.
has super-classes
binding_sitec
has sub-classes
polypeptide_metal_contactc

methioninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001442

A place holder for a cross product with chebi.
has super-classes
amino_acidc

methionine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000223

has super-classes
tRNA_primary_transcriptc

methionyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000266

has super-classes
tRNAc
derives_fromop some methionine_tRNA_primary_transcriptc

methylated_adeninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000161

has super-classes
methylated_DNA_base_featurec
modified_adeninec
has sub-classes
N6_methyladeninec

methylated_cytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000114

has super-classes
methylated_DNA_base_featurec
modified_cytosinec
has sub-classes
4_methylcytosinec, 5_hydroxymethylcytosinec, 5_methylcytosinec

methylated_DNA_base_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000306

has super-classes
modified_DNA_basec
has sub-classes
methylated_adeninec, methylated_cytosinec

methylation_guide_snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005841

Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
has super-classes
C_D_box_snoRNAc
derives_fromop some methylation_guide_snoRNA_primary_transcriptc

methylation_guide_snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000580

has super-classes
snoRNA_primary_transcriptc

methylinosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001233

has super-classes
modified_inosinec

methylwyosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001337

has super-classes
modified_guanosinec

MicF_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000383

has super-classes
antisense_RNAc

microarray_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000328

has super-classes
probec

micronuclear_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000825

is equivalent to
chromosomec and (has_originop some micronuclear_sequencec)
has super-classes
chromosomec
has_originop some micronuclear_sequencec

micronuclear_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000084

has super-classes
organelle_sequencec

microsatellitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000289

has super-classes
satellite_DNAc
has sub-classes
dinucleotide_repeat_microsatellite_featurec, tetranucleotide_repeat_microsatellite_featurec, trinucleotide_repeat_microsatellite_featurec

mini_exon_donor_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000635

has super-classes
primary_transcriptc

mini_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000815

has super-classes
ORFc
has sub-classes
rescue_mini_genec

minicirclec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000980

has super-classes
repliconc

minicircle_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000975

is equivalent to
kinetoplast_genec and (part_ofop some minicirclec)
has super-classes
kinetoplast_genec
part_ofop some minicirclec

minisatellitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000643

has super-classes
satellite_DNAc

minor_TSSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001239

has super-classes
TSSc

minus_10_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000175

Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021.
has super-classes
DNA_motifc
part_ofop some bacterial_RNApol_promoter_sigma_70_elementc
part_ofop some bacterial_RNApol_promoter_sigma_ecf_elementc

minus_12_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001673

has super-classes
DNA_motifc
part_ofop some bacterial_RNApol_promoter_sigma54_elementc

minus_1_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000866

has super-classes
frameshiftc

minus_1_frameshift_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001592

has super-classes
frameshift_variantc

minus_1_translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002329

Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522.
has super-classes
translational_frameshiftc

minus_1_translationally_frameshiftedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001262

has super-classes
translationally_frameshiftedc

minus_24_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001674

has super-classes
DNA_motifc
part_ofop some bacterial_RNApol_promoter_sigma54_elementc

minus_2_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000867

has super-classes
frameshiftc

minus_2_frameshift_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001593

has super-classes
frameshift_variantc

minus_2_translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002330

Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522.
has super-classes
translational_frameshiftc

minus_35_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000176

Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021.
has super-classes
DNA_motifc
part_ofop some bacterial_RNApol_promoter_sigma_ecf_elementc
part_ofop some bacterial_RNApol_promoter_sigma_70_elementc

miR_encoding_lncRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002036

has super-classes
lncRNA_primary_transcriptc
has_partop some pre_miRNAc

miR_encoding_shRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002039

has super-classes
shRNA_primary_transcriptc
has_partop some pre_miRNAc

miR_encoding_snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002034

has super-classes
snoRNA_primary_transcriptc
has_partop some pre_miRNAc

miR_encoding_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002037

has super-classes
tRNA_primary_transcriptc
has_partop some pre_miRNAc

miR_encoding_vaultRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002041

has super-classes
vaultRNA_primary_transcriptc
has_partop some pre_miRNAc

miR_encoding_Y_RNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002043

has super-classes
Y_RNA_primary_transcriptc
has_partop some pre_miRNAc

miRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000276

has super-classes
small_regulatory_ncRNAc
part_ofop some pre_miRNAc
has sub-classes
isomiRc, ref_miRNAc

miRNA_antiguidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001473

has super-classes
miRNA_primary_transcript_regionc

miRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000571

has super-classes
non_protein_codingc

miRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001265

Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
is equivalent to
sncRNA_genec and (has_qualityop some miRNA_encodingc) and (has_qualityop some stRNA_encodingc)
has super-classes
sncRNA_genec
has_qualityop some miRNA_encodingc
has_qualityop some stRNA_encodingc

miRNA_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001246

has super-classes
miRNA_primary_transcript_regionc
part_ofop some pre_miRNAc

miRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000647

has super-classes
nc_primary_transcriptc
has_partop some pre_miRNAc

miRNA_primary_transcript_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001243

has super-classes
primary_transcript_regionc
has sub-classes
miRNA_antiguidec, miRNA_loopc, miRNA_stemc, pre_miRNAc

miRNA_stemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001245

has super-classes
miRNA_primary_transcript_regionc
part_ofop some pre_miRNAc

miRNA_target_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000934

has super-classes
nucleotide_binding_sitec

miRtronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001034

Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
has super-classes
intron_domainc
has_partop some pre_miRNAc

missense_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001583

EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
has super-classes
nonsynonymous_variantc
has sub-classes
conservative_missense_variantc, non_conservative_missense_variantc

MITEc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000338

has super-classes
terminal_inverted_repeat_elementc

mitochondrial_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000819

is equivalent to
chromosomec and (has_originop some mitochondrial_sequencec)
has super-classes
chromosomec
has_originop some mitochondrial_sequencec

mitochondrial_contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001921

Requested by Bayer Cropscience, October, 2012.
is equivalent to
contigc and (has_originop some mitochondrial_sequencec)
has super-classes
contigc
has_originop some mitochondrial_sequencec

mitochondrial_control_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002293

Added as per GitHub Issue Request #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) from INSDC
has super-classes
origin_of_replicationc
has_originop some mitochondrial_sequencec
has sub-classes
mitochondrial_D_loopc

mitochondrial_D_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002294

Added as per request by Terence Murphy (INSDC) for GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)
has super-classes
D_loopc
mitochondrial_control_regionc

mitochondrial_DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001032

This terms is used by MO.
is equivalent to
mitochondrial_sequencec and (has_qualityop some DNAc)
has super-classes
mitochondrial_sequencec
has_qualityop some DNAc

mitochondrial_DNA_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001929

Requested by Bayer Cropscience, October, 2012.
is equivalent to
readc and (has_originop some mitochondrial_DNAc)
has super-classes
readc
has_originop some mitochondrial_DNAc

mitochondrial_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000737

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
organelle_sequencec
has sub-classes
mitochondrial_DNAc

mitochondrial_supercontigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001922

has super-classes
supercontigc

mitochondrial_targeting_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001808

has super-classes
peptide_localization_signalc

mitotic_recombination_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002154

has super-classes
recombination_featurec

MNPc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001013

has super-classes
MNVc

MNVc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002007

has super-classes
substitutionc
has sub-classes
MNPc

MNV_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002179

has super-classes
substitution_artifactc

mobilec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001234

has super-classes
feature_attributec

mobile_element_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002066

has super-classes
deletionc
has sub-classes
Alu_deletionc, HERV_deletionc, LINE1_deletionc, SVA_deletionc

mobile_element_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001837

Requested by the EBI.
is equivalent to
insertionc and (containsop some mobile_genetic_elementc)
has super-classes
insertionc
containsop some mobile_genetic_elementc
has sub-classes
Alu_insertionc, HERV_insertionc, LINE1_insertionc, SVA_insertionc

mobile_genetic_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001037

is equivalent to
regionc and (has_qualityop some mobilec)
has super-classes
biological_regionc
has_qualityop some mobilec
has sub-classes
extrachromosomal_mobile_genetic_elementc, integrated_mobile_genetic_elementc, mobile_intronc

mobile_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000666

is equivalent to
intronc and (has_qualityop some mobilec)
has super-classes
intronc
mobile_genetic_elementc
has_qualityop some mobilec

modified_adeninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001962

has super-classes
modified_DNA_basec
has sub-classes
8_oxoadeninec, methylated_adeninec

modified_adenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001273

has super-classes
modified_RNA_base_featurec
has sub-classes
N6_2_prime_O_dimethyladenosinec, N6_N6_2_prime_O_trimethyladenosinec, N6_N6_dimethyladenosinec, N6_acetyladenosinec, N6_cis_hydroxyisopentenyl_adenosinec, N6_glycinylcarbamoyladenosinec, N6_hydroxynorvalylcarbamoyladenosinec, N6_isopentenyladenosinec, N6_methyl_N6_threonylcarbamoyladenosinec, N6_methyladenosinec, N6_threonylcarbamoyladenosinec, one_methyladenosinec, one_two_prime_O_dimethyladenosinec, two_methyladenosinec, two_methylthio_N6_cis_hydroxyisopentenyl_adenosinec, two_methylthio_N6_hydroxynorvalyl_carbamoyladenosinec, two_methylthio_N6_isopentenyladenosinec, two_methylthio_N6_methyladenosinec, two_methylthio_N6_threonyl_carbamoyladenosinec, two_prime_O_methyladenosinec, two_prime_O_ribosyladenosine_phosphatec

modified_amino_acid_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001385

has super-classes
amino_acidc
has sub-classes
modified_L_alaninec, modified_L_argininec, modified_L_asparaginec, modified_L_aspartic_acidc, modified_L_cysteinec, modified_L_glutamic_acidc, modified_L_glutaminec, modified_L_histidinec, modified_L_isoleucinec, modified_L_leucinec, modified_L_lysinec, modified_L_methioninec, modified_L_phenylalaninec, modified_L_prolinec, modified_L_selenocysteinec, modified_L_serinec, modified_L_threoninec, modified_L_tryptophanc, modified_L_tyrosinec, modified_L_valinec, modified_glycinec

modified_cytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001275

has super-classes
modified_RNA_base_featurec
has sub-classes
N4_2_prime_O_dimethylcytidinec, N4_N4_2_prime_O_trimethylcytidinec, N4_acetyl_2_prime_O_methylcytidinec, N4_acetylcytidinec, N4_methylcytidinec, five_formyl_two_prime_O_methylcytidinec, five_formylcytidinec, five_hydroxymethylcytidinec, five_methylcytidinec, five_two_prime_O_dimethylcytidinec, lysidinec, three_methylcytidinec, two_prime_O_methylcytidinec, two_thiocytidinec

modified_cytosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001963

has super-classes
modified_DNA_basec
has sub-classes
5_carboxylcytosinec, 5_formylcytosinec, methylated_cytosinec

modified_DNA_basec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000305

Modified base:<modified_base>.
has super-classes
basec
epigenetically_modified_regionc
has sub-classes
methylated_DNA_base_featurec, modified_adeninec, modified_cytosinec, modified_guaninec

modified_glycinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001386

has super-classes
modified_amino_acid_featurec

modified_guaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001964

has super-classes
modified_DNA_basec
has sub-classes
8_oxoguaninec

modified_guanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001276

has super-classes
modified_RNA_base_featurec
has sub-classes
N2_2_prime_O_dimethylguanosinec, N2_7_2prirme_O_trimethylguanosinec, N2_7_dimethylguanosinec, N2_N2_2_prime_O_trimethylguanosinec, N2_N2_7_trimethylguanosinec, N2_N2_dimethylguanosinec, N2_methylguanosinec, four_demethylwyosinec, hydroxywybutosinec, isowyosinec, methylwyosinec, one_methylguanosinec, one_two_prime_O_dimethylguanosinec, peroxywybutosinec, seven_deazaguanosinec, seven_methylguanosinec, two_prime_O_methylguanosinec, two_prime_O_ribosylguanosine_phosphatec, undermodified_hydroxywybutosinec, wybutosinec, wyosinec

modified_inosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001274

has super-classes
inosinec
has sub-classes
methylinosinec, one_methylinosinec, one_two_prime_O_dimethylinosinec, two_prime_O_methylinosinec

modified_L_alaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001387

has super-classes
modified_amino_acid_featurec

modified_L_argininec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001406

has super-classes
modified_amino_acid_featurec

modified_L_asparaginec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001388

has super-classes
modified_amino_acid_featurec

modified_L_aspartic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001389

has super-classes
modified_amino_acid_featurec

modified_L_cysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001390

has super-classes
modified_amino_acid_featurec

modified_L_glutamic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001391

has super-classes
modified_amino_acid_featurec

modified_L_glutaminec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001394

has super-classes
modified_amino_acid_featurec

modified_L_histidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001398

has super-classes
modified_amino_acid_featurec

modified_L_isoleucinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001396

has super-classes
modified_amino_acid_featurec

modified_L_leucinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001401

has super-classes
modified_amino_acid_featurec

modified_L_lysinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001400

has super-classes
modified_amino_acid_featurec

modified_L_methioninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001395

has super-classes
modified_amino_acid_featurec

modified_L_phenylalaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001397

has super-classes
modified_amino_acid_featurec

modified_L_prolinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001404

has super-classes
modified_amino_acid_featurec

modified_L_selenocysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001402

has super-classes
modified_amino_acid_featurec

modified_L_serinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001399

has super-classes
modified_amino_acid_featurec

modified_L_threoninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001392

has super-classes
modified_amino_acid_featurec

modified_L_tryptophanc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001393

has super-classes
modified_amino_acid_featurec

modified_L_tyrosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001405

has super-classes
modified_amino_acid_featurec

modified_L_valinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001403

has super-classes
modified_amino_acid_featurec

modified_RNA_base_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000250

has super-classes
basec
has sub-classes
inosinec, modified_adenosinec, modified_cytidinec, modified_guanosinec, modified_uridinec, ribothymidinec, seven_methylguaninec

modified_uridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001277

has super-classes
modified_RNA_base_featurec
has sub-classes
dihydrouridinec, five_aminomethyl_two_thiouridinec, five_carbamoylmethyl_two_prime_O_methyluridinec, five_carbamoylmethyluridinec, five_carboxyhydroxymethyl_uridinec, five_carboxyhydroxymethyl_uridine_methyl_esterc, five_carboxymethylaminomethyl_two_prime_O_methyluridinec, five_carboxymethylaminomethyl_two_thiouridinec, five_carboxymethylaminomethyluridinec, five_carboxymethyluridinec, five_hydroxyuridinec, five_isopentenylaminomethyl_two_prime_O_methyluridinec, five_isopentenylaminomethyl_two_thiouridinec, five_isopentenylaminomethyl_uridinec, five_methoxycarbonylmethyl_two_prime_O_methyluridinec, five_methoxycarbonylmethyl_two_thiouridinec, five_methoxycarbonylmethyluridinec, five_methoxyuridinec, five_methyl_2_thiouridinec, five_methylaminomethyl_two_selenouridinec, five_methylaminomethyl_two_thiouridinec, five_methylaminomethyluridinec, five_methyldihydrouridinec, five_methyluridinec, five_taurinomethyl_two_thiouridinec, five_taurinomethyluridinec, five_two_prime_O_dimethyluridinec, four_thiouridinec, one_methyl_three_three_amino_three_carboxypropyl_pseudouridinec, one_methylpseudouridinec, pseudouridinec, three_methylpseudouridinec, three_methyluridinec, three_three_amino_three_carboxypropyl_uridinec, three_two_prime_O_dimethyluridinec, two_prime_O_methylpseudouridinec, two_prime_O_methyluridinec, two_thio_two_prime_O_methyluridinec, two_thiouridinec, uridine_five_oxyacetic_acidc, uridine_five_oxyacetic_acid_methyl_esterc

molecular_contact_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100002

Range.
has super-classes
biochemical_region_of_peptidec
has sub-classes
polypeptide_DNA_contactc, polypeptide_ligand_contactc, polypeptide_metal_contactc, protein_protein_contactc

monocistronicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000878

has super-classes
transcript_attributec

monocistronic_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000633

is equivalent to
mRNAc and (has_qualityop some monocistronicc)
has super-classes
mRNAc
monocistronic_transcriptc
has_qualityop some monocistronicc

monocistronic_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000632

is equivalent to
primary_transcriptc and (has_qualityop some monocistronicc)
has super-classes
primary_transcriptc
monocistronic_transcriptc
has_qualityop some monocistronicc

monocistronic_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000665

is equivalent to
transcriptc and (has_qualityop some monocistronicc)
has super-classes
transcriptc
has_qualityop some monocistronicc
has sub-classes
monocistronic_mRNAc, monocistronic_primary_transcriptc

monomeric_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001934

has super-classes
tandem_repeatc

moRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002032

MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do. Requested by Thomas Desvignes, Jan 2015.
has super-classes
small_regulatory_ncRNAc
part_ofop some pre_miRNAc

morpholino_backbonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001183

Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
has super-classes
nucleic_acidc

morpholino_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000034

is equivalent to
synthetic_oligoc and (has_qualityop some morpholino_backbonec)
has super-classes
synthetic_oligoc
has_qualityop some morpholino_backbonec

mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000234

An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
mature_transcriptc
has sub-classes
NSD_transcriptc, capped_mRNAc, circular_mRNAc, consensus_mRNAc, edited_mRNAc, exemplar_mRNAc, mRNA_with_frameshiftc, monocistronic_mRNAc, polyadenylated_mRNAc, polycistronic_mRNAc, recoded_mRNAc, trans_spliced_mRNAc

mRNA_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000863

has super-classes
transcript_attributec
has sub-classes
exemplarc, frameshiftc, inframec, polyadenylatedc, recodedc

mRNA_by_polyadenylation_statusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000245

mRNA_contigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001829

Requested by Bayer Cropscience June, 2011.
has super-classes
contigc

mRNA_not_polyadenylatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000247

mRNA_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001827

Requested by Bayer Cropscience June, 2011.
has super-classes
readc

mRNA_recoded_by_codon_redefinitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001265

is equivalent to
mRNAc and (has_qualityop some codon_redefinedc)
has super-classes
recoded_mRNAc
has_qualityop some codon_redefinedc

mRNA_recoded_by_translational_bypassc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001264

is equivalent to
mRNAc and (has_qualityop some recoded_by_translational_bypassc)
has super-classes
recoded_mRNAc
has_qualityop some recoded_by_translational_bypassc

mRNA_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000836

This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
has super-classes
mature_transcript_regionc
part_ofop some mRNAc
has sub-classes
CDSc, CDS_regionc, RNA_thermometerc, UTRc, UTR_regionc, five_prime_open_reading_framec, recoding_stimulatory_regionc, ribosome_entry_sitec, riboswitchc, translational_frameshiftc

mRNA_with_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000108

is equivalent to
mRNAc and (has_qualityop some frameshiftc)
has super-classes
mRNAc
has_qualityop some frameshiftc
has sub-classes
mRNA_with_minus_1_frameshiftc, mRNA_with_minus_2_frameshiftc, mRNA_with_plus_1_frameshiftc, mRNA_with_plus_2_frameshiftc

mRNA_with_minus_1_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000282

is equivalent to
mRNA_with_frameshiftc and (has_qualityop some minus_1_frameshiftc)
has super-classes
mRNA_with_frameshiftc
has_qualityop some minus_1_frameshiftc

mRNA_with_minus_2_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000335

is equivalent to
mRNA_with_frameshiftc and (has_qualityop some minus_2_frameshiftc)
has super-classes
mRNA_with_frameshiftc
has_qualityop some minus_2_frameshiftc

mRNA_with_plus_1_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000321

is equivalent to
mRNA_with_frameshiftc and (has_qualityop some plus_1_frameshiftc)
has super-classes
mRNA_with_frameshiftc
has_qualityop some plus_1_frameshiftc

mRNA_with_plus_2_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000329

is equivalent to
mRNA_with_frameshiftc and (has_qualityop some plus_2_framshiftc)
has super-classes
mRNA_with_frameshiftc
has_qualityop some plus_2_framshiftc

mt_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000088

is equivalent to
genec and (has_originop some mitochondrial_sequencec)
has super-classes
genec
has_originop some mitochondrial_sequencec
has sub-classes
kinetoplast_genec

mt_LSU_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002345

Added as a request from EMBL. See GitHub Issue #493
has super-classes
mt_rRNAc

mt_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002128

Updated definition to be consistent with format of other rRNA definitions on 10 June 2021. Requested by EBI. See GitHub Issue #493.
has super-classes
rRNAc
has sub-classes
mt_LSU_rRNAc, mt_SSU_rRNAc

mt_SSU_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002344

Added as a request from EMBL. See GitHub Issue #493
has super-classes
mt_rRNAc

mt_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002129

has super-classes
tRNAc

MTEc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001162

has super-classes
core_eukaryotic_promoter_elementc
part_ofop some RNApol_II_core_promoterc

multiplexing_sequence_identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002023

has super-classes
tagc

mutated_variant_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001148

Discrete.
has super-classes
polypeptide_variation_sitec

mutation_causing_inframe_polypeptide_N_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000106

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_out_of_frame_polypeptide_C_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000109

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_out_of_frame_polypeptide_N_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000107

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_polypeptide_C_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000101

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_polypeptide_N_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000100

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutational_hotspotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002186

has super-classes
biological_regionc

mutaton_causing_inframe_polypeptide_C_terminal_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000108

Mutator_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002280

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

N2_2_prime_O_dimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001329

has super-classes
modified_guanosinec

N2_7_2prirme_O_trimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001343

has super-classes
modified_guanosinec

N2_7_dimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001338

has super-classes
modified_guanosinec

N2_methylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001325

has super-classes
modified_guanosinec

N2_N2_2_prime_O_trimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001330

has super-classes
modified_guanosinec

N2_N2_7_trimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001339

has super-classes
modified_guanosinec

N2_N2_dimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001328

has super-classes
modified_guanosinec

N4_2_prime_O_dimethylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001291

has super-classes
modified_cytidinec

N4_acetyl_2_prime_O_methylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001288

has super-classes
modified_cytidinec

N4_acetylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001285

has super-classes
modified_cytidinec

N4_methylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001290

has super-classes
modified_cytidinec

N4_N4_2_prime_O_trimethylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001294

has super-classes
modified_cytidinec

N6_2_prime_O_dimethyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001312

has super-classes
modified_adenosinec

N6_acetyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001315

has super-classes
modified_adenosinec

N6_cis_hydroxyisopentenyl_adenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001302

has super-classes
modified_adenosinec

N6_glycinylcarbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001304

has super-classes
modified_adenosinec

N6_hydroxynorvalylcarbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001308

has super-classes
modified_adenosinec

N6_isopentenyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001300

has super-classes
modified_adenosinec

N6_methyl_N6_threonylcarbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001307

has super-classes
modified_adenosinec

N6_methyladeninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001920

has super-classes
methylated_adeninec

N6_methyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001297

has super-classes
modified_adenosinec

N6_N6_2_prime_O_trimethyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001313

has super-classes
modified_adenosinec

N6_N6_dimethyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001311

has super-classes
modified_adenosinec

N6_threonylcarbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001305

has super-classes
modified_adenosinec

N_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001835

has super-classes
vertebrate_immune_system_gene_recombination_featurec

n_terminal_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100014

has super-classes
cleaved_peptide_regionc
part_ofop some signal_peptidec

naturalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000782

has super-classes
feature_attributec

natural_plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001476

is equivalent to
plasmidc and (has_qualityop some naturalc)
has super-classes
plasmidc
extrachromosomal_mobile_genetic_elementc
has_qualityop some naturalc

natural_transposable_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000797

is equivalent to
transposable_elementc and (has_qualityop some naturalc)
has super-classes
transposable_elementc
extrachromosomal_mobile_genetic_elementc
has_qualityop some naturalc

natural_variant_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001147

Discrete.
has super-classes
polypeptide_variation_sitec

nc_conserved_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000334

has super-classes
conserved_regionc

nc_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000483

has super-classes
primary_transcriptc
has sub-classes
SRP_RNA_primary_transcriptc, Y_RNA_primary_transcriptc, lncRNA_primary_transcriptc, miRNA_primary_transcriptc, rRNA_primary_transcriptc, scRNA_primary_transcriptc, shRNA_primary_transcriptc, snRNA_primary_transcriptc, snoRNA_primary_transcriptc, tRNA_primary_transcriptc, tasiRNA_primary_transcriptc, tmRNA_primary_transcriptc, vaultRNA_primary_transcriptc

ncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000655

A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
has super-classes
mature_transcriptc
has sub-classes
RNA_7SKc, RNase_MRP_RNAc, RNase_P_RNAc, SRP_RNAc, Y_RNAc, antisense_RNAc, circular_ncRNAc, class_II_RNAc, class_I_RNAc, enhancerRNAc, guide_RNAc, lncRNAc, priRNAc, rRNAc, rRNA_cleavage_RNAc, rasiRNAc, scRNAc, shRNAc, sncRNAc, tasiRNAc, telomerase_RNAc, telomeric_transcriptc, three_prime_overlapping_ncrnac, vault_RNAc

ncRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001263

has super-classes
genec
has sub-classes
RNA_7SK_genec, RNase_MRP_RNA_genec, RNase_P_RNA_genec, SRP_RNA_genec, enzymatic_RNA_genec, gRNA_genec, lncRNA_genec, rRNA_genec, scRNA_genec, sncRNA_genec, telomerase_RNA_genec

NDM2_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001167

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

NDM3_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001168

has super-classes
promoter_elementc
part_ofop some RNApol_II_promoterc

negative_sense_ssRNA_viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001200

has super-classes
ss_RNA_viral_sequencec

negatively_autoregulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000473

has super-classes
transcriptionally_repressedc
autoregulatedc

negatively_autoregulated_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000891

is equivalent to
genec and (has_qualityop some negatively_autoregulatedc)
has super-classes
genec
has_qualityop some negatively_autoregulatedc

nested_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001051

nested_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001052

nested_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001649

has super-classes
repeat_regionc
has sub-classes
nested_tandem_repeatc

nested_tandem_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001658

Tracker ID: 3052459.
has super-classes
nested_repeatc

nested_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001053

nested_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001648

has super-classes
transposable_elementc

Ngaro_YR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002288

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
YR_retrotransposonc

NMD_escaping_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002320

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
functionally_abnormalc
has sub-classes
frameshift_variant_NMD_escapingc, splice_acceptor_variant_NMD_escapingc, splice_donor_variant_NMD_escapingc, stop_gained_NMD_escapingc

NMD_polymorphic_pseudogene_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002118

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
NMD_transcriptc

NMD_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002114

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
protein_coding_primary_transcriptc
has sub-classes
NMD_polymorphic_pseudogene_transcriptc

NMD_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001621

has super-classes
transcript_variantc

NMD_triggering_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002319

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
functionally_abnormalc
has sub-classes
frameshift_variant_NMD_triggeringc, splice_acceptor_variant_NMD_triggeringc, splice_donor_variant_NMD_triggeringc, stop_gained_NMD_triggeringc

no_outputc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100010

has super-classes
experimental_result_regionc

no_sequence_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002073

This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly.
has super-classes
sequence_comparisonc

non_adjacent_residuesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001083

has super-classes
polypeptide_sequencing_informationc

non_allelic_homologous_recombination_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002094

has super-classes
recombination_hotspotc

non_AUG_initiated_uORFc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002151

has super-classes
uORFc

non_canonical_five_prime_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000679

has super-classes
five_prime_cis_splice_sitec

non_canonical_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000674

non_canonical_start_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000680

has super-classes
start_codonc
has sub-classes
CTG_start_codonc, four_bp_start_codonc

non_canonical_three_prime_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000678

has super-classes
three_prime_cis_splice_sitec

non_capped_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000106

non_coding_transcript_exon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001792

has super-classes
non_coding_transcript_variantc
exon_variantc

non_coding_transcript_intron_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001970

has super-classes
non_coding_transcript_variantc
intron_variantc

non_coding_transcript_splice_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002088

has super-classes
non_coding_transcript_variantc
splice_region_variantc

non_coding_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001619

Within non-coding gene - Located within a gene that does not code for a protein.
has super-classes
transcript_variantc
has sub-classes
mature_miRNA_variantc, non_coding_transcript_exon_variantc, non_coding_transcript_intron_variantc, non_coding_transcript_splice_region_variantc

non_complimentary_stemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002256

Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
has super-classes
stemc

non_conservative_amino_acid_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001608

has super-classes
amino_acid_substitutionc

non_conservative_missense_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001586

has super-classes
missense_variantc
has sub-classes
rare_amino_acid_variantc

non_covalent_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001091

Discrete.

non_cytoplasmic_polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001074

This could be inside an organelle within the cell.
has super-classes
extramembrane_polypeptide_regionc

non_LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000189

has super-classes
retrotransposonc
has sub-classes
LINE_elementc, Penelope_retrotransposonc, SINE_elementc, YR_retrotransposonc

non_LTR_retrotransposon_polymeric_tractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000433

has super-classes
repeat_regionc
repeat_componentc
part_ofop some non_LTR_retrotransposonc

non_processed_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001760

has super-classes
pseudogenec
has sub-classes
cassette_pseudogenec, duplicated_pseudogenec, nuclear_mt_pseudogenec, pseudogene_by_unequal_crossing_overc, transcribed_unprocessed_pseudogenec, translated_unprocessed_pseudogenec, unitary_pseudogenec

non_protein_codingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000011

has super-classes
gene_attributec
has sub-classes
SRP_RNA_encodingc, gRNA_encodingc, miRNA_encodingc, rRNA_encodingc, scRNA_encodingc, snRNA_encodingc, snoRNA_encodingc, stRNA_encodingc, tRNA_encodingc, tmRNA_encodingc

non_synonymousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001816

has super-classes
coding_variant_qualityc

non_terminal_residuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001084

Discrete.
has super-classes
polypeptide_sequencing_informationc

non_transcribed_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000183

has super-classes
gene_component_regionc

nonamer_of_recombination_feature_of_vertebrate_immune_system_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000562

has super-classes
vertebrate_immune_system_gene_recombination_signal_featurec
has sub-classes
J_nonamerc, V_nonamerc, five_prime_D_nonamerc, three_prime_D_nonamerc

noncoding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000198

has super-classes
exonc
has sub-classes
five_prime_noncoding_exonc, three_prime_noncoding_exonc

noncoding_region_of_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001214

An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
has super-classes
exon_regionc
has sub-classes
five_prime_coding_exon_noncoding_regionc, three_prime_coding_exon_noncoding_regionc

noncontiguous_finishedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001490

has super-classes
whole_genome_sequence_statusc

nonsynonymous_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001992

has super-classes
inframe_variantc
has sub-classes
missense_variantc, redundant_inserted_stop_gainedc, start_lostc, stop_gainedc, stop_lostc

novel_sequence_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001838

Requested by the NCBI.
has super-classes
insertionc

NSD_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002130

has super-classes
mRNAc

nuclear_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000828

is equivalent to
chromosomec and (has_originop some nuclear_sequencec)
has super-classes
chromosomec
has_originop some nuclear_sequencec

nuclear_export_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001531

has super-classes
peptide_localization_signalc

nuclear_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000087

is equivalent to
genec and (has_originop some nuclear_sequencec)
has super-classes
genec
has_originop some nuclear_sequencec

nuclear_localization_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001528

has super-classes
peptide_localization_signalc

nuclear_mitochondrialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000899

nuclear_mt_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001044

Definition change requested by Val, 3172757.
has super-classes
non_processed_pseudogenec

nuclear_rim_localization_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001534

has super-classes
peptide_localization_signalc

nuclear_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000738

Moved from is_a SO:0000736 (organelle_sequence) when brought to our attention by GitHub issue #489.
has super-classes
sequence_locationc

nuclease_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000059

has super-classes
nucleotide_to_protein_binding_sitec
has sub-classes
homing_endonuclease_binding_sitec, nuclease_sensitive_sitec, restriction_enzyme_binding_sitec

nuclease_hypersensitive_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000322

Relationship to accessible_DNA_region added 11 Feb 2021. GREEKC pointed out that this is an assay based term, but we need a biological term for the accessible DNA. See GitHub Issue #531.
has super-classes
nuclease_sensitive_sitec
accessible_DNA_regionc
has sub-classes
DNaseI_hypersensitive_sitec

nuclease_sensitive_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000684

has super-classes
nuclease_binding_sitec
has sub-classes
group_1_intron_homing_endonuclease_target_regionc, nuclease_hypersensitive_sitec

nucleic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000348

has super-classes
polymer_attributec
has sub-classes
DNAc, GNAc, LNAc, PNAc, RNAc, TNAc, morpholino_backbonec

nucleomorph_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000097

is equivalent to
genec and (has_originop some nucleomorphic_sequencec)
has super-classes
genec
has_originop some nucleomorphic_sequencec

nucleomorphic_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000829

is equivalent to
chromosomec and (has_originop some nucleomorphic_sequencec)
has super-classes
chromosomec
has_originop some nucleomorphic_sequencec

nucleomorphic_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000739

has super-classes
organelle_sequencec

nucleotide_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001655

See GO:0000166 : nucleotide binding.
has super-classes
binding_sitec
has sub-classes
DNA_binding_sitec, miRNA_target_sitec, primer_binding_sitec

nucleotide_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002204

has super-classes
junctionc
has sub-classes
restriction_enzyme_cleavage_junctionc

nucleotide_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000347

has super-classes
matchc
has sub-classes
cross_genome_matchc, expressed_sequence_matchc, primer_matchc, translated_nucleotide_matchc

nucleotide_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000714

has super-classes
sequence_motifc
has sub-classes
DNA_motifc, RNA_motifc

nucleotide_to_protein_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001654

has super-classes
protein_binding_sitec
has sub-classes
TF_binding_sitec, enhancer_binding_sitec, histone_binding_sitec, insulator_binding_sitec, nuclease_binding_sitec

null_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002055

has super-classes
functionally_abnormalc
has sub-classes
absent_gene_productc

ochre_stop_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002334

Added as per GitHub request #537.
has super-classes
stop_codonc

octamer_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001258

Nature. 1986 Oct 16-22;323(6089):640-3.
has super-classes
DNA_motifc
part_ofop some RNApol_II_promoterc

Okazaki_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001985

Requested by Midori Harris, 2013.
has super-classes
biological_regionc

oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000696

has super-classes
reagentc
has sub-classes
DNAzymec, aptamerc, ds_oligoc, probec, sgRNAc, ss_oligoc, synthetic_oligoc, tagc

oligo_U_tailc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000609

has super-classes
biological_regionc
adjacent_toop some guide_RNAc

one_methyl_three_three_amino_three_carboxypropyl_pseudouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001373

has super-classes
modified_uridinec

one_methyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001295

has super-classes
modified_adenosinec

one_methylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001324

has super-classes
modified_guanosinec

one_methylinosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001278

has super-classes
modified_inosinec

one_methylpseudouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001347

has super-classes
modified_uridinec

one_two_prime_O_dimethyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001314

has super-classes
modified_adenosinec

one_two_prime_O_dimethylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001340

has super-classes
modified_guanosinec

one_two_prime_O_dimethylinosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001279

has super-classes
modified_inosinec

opal_stop_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002335

Added as per GitHub request #537.
has super-classes
stop_codonc

open_chromatin_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001747

Requested by John Calley 3125900.
has super-classes
biological_regionc

operatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000057

Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.
has super-classes
transcriptional_cis_regulatory_regionc

operonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000178

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020.
has super-classes
gene_groupc
has sub-classes
complex_operonc, simple_operonc

operon_memberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000080

has super-classes
gene_array_memberc

ORFc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000236

The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
reading_framec
has sub-classes
mini_genec, sORFc, tnaORFc, uORFc

organelle_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000736

has super-classes
sequence_locationc
has sub-classes
macronuclear_sequencec, micronuclear_sequencec, mitochondrial_sequencec, nucleomorphic_sequencec, plastid_sequencec

oriCc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000953

has super-classes
origin_of_replicationc

origin_of_replicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000296

has super-classes
biological_regionc
part_ofop some repliconc
has sub-classes
ARSc, amplification_originc, early_origin_of_replicationc, late_origin_of_replicationc, mitochondrial_control_regionc, oriCc, oriTc, oriVc, replication_start_sitec, telomeric_D_loopc

oriTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000724

has super-classes
origin_of_replicationc

oriVc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000952

has super-classes
origin_of_replicationc

orphanc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000910

has super-classes
predictedc

orphan_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001247

is equivalent to
CDS_predictedc and (has_originop some orphanc)
has super-classes
CDS_predictedc
has_originop some orphanc

orthologousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000858

has super-classes
homologousc

orthologous_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000855

This term should be used in conjunction with the similarity relationships defined in SO.
is equivalent to
homologous_regionc and (has_qualityop some orthologousc)
has super-classes
homologous_regionc
has_qualityop some orthologousc

outronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001475

has super-classes
primary_transcript_regionc

overlappingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000068

has super-classes
gene_to_gene_featurec
has sub-classes
antisensec, five_prime_five_prime_overlapc, five_prime_three_prime_overlapc, inside_intronc, three_prime_five_prime_overlapc, three_prime_three_prime_overlapc

overlapping_EST_setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001262

has super-classes
overlapping_feature_setc
has_partop some ESTc

overlapping_feature_setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001261

This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
has super-classes
experimental_result_regionc
has sub-classes
overlapping_EST_setc

OxyS_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000384

has super-classes
small_regulatory_ncRNAc

P_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001535

Moved from under DNA_transposon (SO:0000182) by Dave Sant as per request from GitHub issue #488 on June 25, 2020
has super-classes
terminal_inverted_repeat_elementc

PACc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000154

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
has super-classes
vector_repliconc

PAC_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000762

PAC_endc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001480

has super-classes
readc
part_ofop some PACc

paired_end_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001790

has super-classes
assembly_componentc

paracentricc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001519

has super-classes
inversion_attributec

paracentric_inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000047

is equivalent to
chromosomal_inversionc and (has_qualityop some paracentricc)
has super-classes
chromosomal_inversionc
has_qualityop some paracentricc

parallel_beta_strandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001113

Range.
has super-classes
beta_strandc

paralogousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000859

has super-classes
homologousc

paralogous_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000854

A term to be used in conjunction with the paralogous_to relationship.
is equivalent to
homologous_regionc and (has_qualityop some paralogousc)
has super-classes
homologous_regionc
has_qualityop some paralogousc

partial_genomic_sequence_assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001876

Requested by Bayer Cropscience January, 2012.
has super-classes
sequence_assemblyc
has sub-classes
supercontigc, ultracontigc

partially_characterized_chromosomal_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000175

has super-classes
uncharacterized_chromosomal_mutationc

partially_duplicated_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002244

Added as per request from the Illumina group
has super-classes
transcript_variantc
has sub-classes
five_prime_duplicated_transcriptc, three_prime_duplicated_transcriptc

partially_processed_cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000813

is equivalent to
invalidated_cDNA_clonec and (has_qualityop some invalidated_by_partial_processingc)
has super-classes
invalidated_cDNA_clonec
has_qualityop some invalidated_by_partial_processingc

paternal_uniparental_disomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001746

has super-classes
UPDc

paternal_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001776

has super-classes
variant_originc

paternally_imprintedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000136

has super-classes
genomically_imprintedc

paternally_imprinted_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000889

is equivalent to
genec and (has_qualityop some paternally_imprintedc)
has super-classes
epigenetically_modified_genec
has_qualityop some paternally_imprintedc

pathogenic_islandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000773

Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
has super-classes
genomic_islandc

PCBc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001871

has super-classes
promoter_elementc

PCR_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000006

This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
has super-classes
reagentc
has sub-classes
AFLP_fragmentc, RAPDc

pedigree_specific_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001779

has super-classes
variant_originc

Penelope_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002290

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
non_LTR_retrotransposonc

peptide_coilc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100012

has super-classes
polypeptide_secondary_structurec

peptide_collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001501

Term requested via tracker ID: 2910829.
is equivalent to
sequence_collectionc and (has_partop some polypeptidec)
has super-classes
sequence_collectionc
has_partop some polypeptidec

peptide_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001114

Range.
has super-classes
polypeptide_secondary_structurec
has sub-classes
left_handed_peptide_helixc, right_handed_peptide_helixc, transmembrane_helixc

peptide_localization_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001527

has super-classes
polypeptide_regionc
has sub-classes
ER_retention_signalc, endosomal_localization_signalc, lysosomal_localization_signalc, mitochondrial_targeting_signalc, nuclear_export_signalc, nuclear_localization_signalc, nuclear_rim_localization_signalc, signal_peptidec, transit_peptidec, vacuolar_sorting_signalc

peptidylc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001407

has super-classes
polymer_attributec

pericentricc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001518

has super-classes
inversion_attributec

pericentric_inversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000046

is equivalent to
chromosomal_inversionc and (has_qualityop some pericentricc)
has super-classes
chromosomal_inversionc
has_qualityop some pericentricc

peroxywybutosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001333

has super-classes
modified_guanosinec

Phage_RNA_Polymerase_Promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001204

former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.
has super-classes
viral_promoterc
has sub-classes
SP6_RNA_Polymerase_Promoterc, T3_RNA_Polymerase_Promoterc, T7_RNA_Polymerase_Promoterc

phage_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001042

has super-classes
viral_sequencec

phagemidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000157

has super-classes
vector_repliconc

phagemid_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000761

phenylalaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001441

A place holder for a cross product with chebi.
has super-classes
amino_acidc

phenylalanine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000224

has super-classes
tRNA_primary_transcriptc

phenylalanyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000267

has super-classes
tRNAc
derives_fromop some phenylalanine_tRNA_primary_transcriptc

pheromone_response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002045

Requested by Rama, SGD.
has super-classes
TF_binding_sitec
promoter_elementc

Pho7_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002216

has super-classes
promoter_elementc

phosphorylation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001811

has super-classes
post_translationally_modified_regionc

pi_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001118

Range.
has super-classes
right_handed_peptide_helixc

PIF_Harbinger_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002284

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

piggyBac_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002283

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

PIP_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001810

has super-classes
protein_protein_contactc

piRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001035

has super-classes
small_regulatory_ncRNAc

piRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001638

Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
has super-classes
sncRNA_genec

plasmidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000155

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
repliconc
has sub-classes
circular_plasmidc, engineered_plasmidc, episomec, linear_plasmidc, natural_plasmidc

plasmid_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000759

plasmid_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000098

is equivalent to
genec and (has_originop some plasmid_locationc)
has super-classes
genec
has_originop some plasmid_locationc

plasmid_locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000749

has super-classes
sequence_locationc

plasmid_vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000755

is equivalent to
repliconc and (derives_fromop some plasmidc)
has super-classes
vector_repliconc
derives_fromop some plasmidc

plastid_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000090

is equivalent to
genec and (has_originop some plastid_sequencec)
has super-classes
genec
has_originop some plastid_sequencec
has sub-classes
apicoplast_genec, chromoplast_genec, ct_genec, cyanelle_genec, leucoplast_genec, proplastid_genec

plastid_LSU_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002348

Added as a request from EMBL. See GitHub Issue #493
has super-classes
plastid_rRNAc

plastid_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002346

Added as a request from EMBL. See GitHub Issue #493
has super-classes
rRNAc
has sub-classes
plastid_LSU_rRNAc, plastid_SSU_rRNAc

plastid_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000740

has super-classes
organelle_sequencec
has sub-classes
apicoplast_sequencec, chloroplast_sequencec, chromoplast_sequencec, cyanelle_sequencec, leucoplast_sequencec, proplastid_sequencec

plastid_SSU_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002347

Added as a request from EMBL. See GitHub Issue #493
has super-classes
plastid_rRNAc

plus_1_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000868

has super-classes
frameshiftc

plus_1_frameshift_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001594

has super-classes
frameshift_variantc

plus_1_translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001211

has super-classes
translational_frameshiftc

plus_1_translationally_frameshiftedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001263

has super-classes
translationally_frameshiftedc

plus_2_frameshift_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001595

has super-classes
frameshift_variantc

plus_2_framshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000869

has super-classes
frameshiftc

plus_2_translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001212

has super-classes
translational_frameshiftc

PNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001184

Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
has super-classes
nucleic_acidc

PNA_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001011

is equivalent to
synthetic_oligoc and (has_qualityop some PNAc)
has super-classes
synthetic_oligoc
has_qualityop some PNAc

point_centromerec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001794

has super-classes
centromerec

point_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000008

has super-classes
SNVc

polintonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001170

has super-classes
terminal_inverted_repeat_elementc

polyA_primed_cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000812

is equivalent to
invalidated_cDNA_clonec and (has_qualityop some invalidated_by_genomic_polyA_primed_cDNAc)
has super-classes
invalidated_cDNA_clonec
has_qualityop some invalidated_by_genomic_polyA_primed_cDNAc

polyA_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000610

has super-classes
biological_regionc
adjacent_toop some mRNAc

polyA_signal_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000551

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc

polyA_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000553

has super-classes
junctionc
part_ofop some mature_transcriptc
part_ofop some three_prime_UTRc

polyA_site_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002259

Added as per GitHub Issue Request #450 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/450)
has super-classes
biological_regionc
has_partop some polyA_sitec
part_ofop some three_prime_UTRc

polyadenylatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000246

has super-classes
mRNA_attributec

polyadenylated_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000871

is equivalent to
mRNAc and (adjacent_toop some polyA_sequencec) and (has_qualityop some polyadenylatedc)
has super-classes
mRNAc
adjacent_toop some polyA_sequencec
has_qualityop some polyadenylatedc

polyadenylation_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001545

has super-classes
transcript_processing_variantc
has sub-classes
decreased_polyadenylation_variantc, increased_polyadenylation_variantc

polycistronicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000880

has super-classes
transcript_attributec
has sub-classes
dicistronicc

polycistronic_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000477

polycistronic_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000634

is equivalent to
mRNAc and (has_qualityop some polycistronicc)
has super-classes
polycistronic_transcriptc
mRNAc
has_qualityop some polycistronicc
has sub-classes
dicistronic_mRNAc

polycistronic_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000631

is equivalent to
primary_transcriptc and (has_qualityop some polycistronicc)
has super-classes
polycistronic_transcriptc
primary_transcriptc
has_qualityop some polycistronicc
has sub-classes
dicistronic_primary_transcriptc

polycistronic_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000078

is equivalent to
transcriptc and (has_qualityop some polycistronicc)
has super-classes
transcriptc
has_qualityop some polycistronicc
has sub-classes
dicistronic_transcriptc, polycistronic_mRNAc, polycistronic_primary_transcriptc

polymer_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000443

has super-classes
sequence_attributec
has sub-classes
nucleic_acidc, peptidylc, synthetic_sequencec, topology_attributec

polymerase_synthesis_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001426

An example is a read produced by Illumina technology.
has super-classes
readc

polymorphic_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001841

This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
has super-classes
pseudogenec
has sub-classes
polymorphic_pseudogene_with_retained_intronc

polymorphic_pseudogene_processed_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002116

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
pseudogene_processed_transcriptc

polymorphic_pseudogene_with_retained_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002110

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
polymorphic_pseudogenec

polymorphic_sequence_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001025

has super-classes
allelec

polymorphic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001766

has super-classes
variant_frequencyc

polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000104

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
has super-classes
biological_regionc
derives_fromop some CDSc

polypeptide_binding_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100018

has super-classes
biochemical_region_of_peptidec

polypeptide_calcium_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001094

Residue involved in contact with calcium.
has super-classes
polypeptide_metal_contactc

polypeptide_catalytic_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100019

has super-classes
biochemical_region_of_peptidec

polypeptide_cobalt_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001095

has super-classes
polypeptide_metal_contactc

polypeptide_conserved_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100017

has super-classes
polypeptide_motifc
has sub-classes
CAAX_boxc, KEN_boxc, SHP_boxc, destruction_boxc

polypeptide_conserved_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100021

has super-classes
polypeptide_regionc
has sub-classes
polypeptide_domainc, polypeptide_motifc, polypeptide_repeatc

polypeptide_copper_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001096

has super-classes
polypeptide_metal_contactc

polypeptide_DNA_contactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100020

has super-classes
DNA_binding_sitec
molecular_contact_regionc

polypeptide_domainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000417

Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
has super-classes
polypeptide_structural_regionc
polypeptide_conserved_regionc

polypeptide_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001554

has super-classes
translational_product_function_variantc
has sub-classes
polypeptide_gain_of_function_variantc, polypeptide_localization_variantc, polypeptide_loss_of_function_variantc, polypeptide_post_translational_processing_variantc

polypeptide_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001616

has super-classes
polypeptide_sequence_variantc

polypeptide_gain_of_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001557

has super-classes
polypeptide_function_variantc

polypeptide_iron_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001097

has super-classes
polypeptide_metal_contactc

polypeptide_ligand_contactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001105

has super-classes
ligand_binding_sitec
molecular_contact_regionc

polypeptide_localization_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001558

has super-classes
polypeptide_function_variantc

polypeptide_loss_of_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001559

has super-classes
polypeptide_function_variantc
has sub-classes
inactive_ligand_binding_sitec, polypeptide_partial_loss_of_functionc

polypeptide_magnesium_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001098

has super-classes
polypeptide_metal_contactc

polypeptide_manganese_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001099

has super-classes
polypeptide_metal_contactc

polypeptide_metal_contactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001092

Residue is part of a binding site for a metal ion.
has super-classes
metal_binding_sitec
molecular_contact_regionc
has sub-classes
polypeptide_calcium_ion_contact_sitec, polypeptide_cobalt_ion_contact_sitec, polypeptide_copper_ion_contact_sitec, polypeptide_iron_ion_contact_sitec, polypeptide_magnesium_ion_contact_sitec, polypeptide_manganese_ion_contact_sitec, polypeptide_molybdenum_ion_contact_sitec, polypeptide_nickel_ion_contact_sitec, polypeptide_tungsten_ion_contact_sitec, polypeptide_zinc_ion_contact_sitec

polypeptide_molybdenum_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001100

has super-classes
polypeptide_metal_contactc

polypeptide_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001067

Range.
has super-classes
polypeptide_conserved_regionc
has sub-classes
biochemical_region_of_peptidec, polypeptide_conserved_motifc

polypeptide_nest_left_right_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001121

has super-classes
polypeptide_nest_motifc

polypeptide_nest_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001120

has super-classes
polypeptide_secondary_structurec
has sub-classes
polypeptide_nest_left_right_motifc, polypeptide_nest_right_left_motifc

polypeptide_nest_right_left_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001122

has super-classes
polypeptide_nest_motifc

polypeptide_nickel_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001101

has super-classes
polypeptide_metal_contactc

polypeptide_partial_loss_of_functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001561

has super-classes
polypeptide_loss_of_function_variantc

polypeptide_post_translational_processing_affectedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000123

polypeptide_post_translational_processing_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001562

has super-classes
polypeptide_function_variantc

polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000839

Added to allow the polypeptide regions to have is_a paths back to the root.
has super-classes
biological_regionc
part_ofop some polypeptidec
has sub-classes
2A_self_cleaving_peptide_regionc, cleaved_peptide_regionc, compositionally_biased_region_of_peptidec, hydrophobic_region_of_peptidec, immature_peptide_regionc, immunoglobulin_regionc, mature_protein_regionc, peptide_localization_signalc, polypeptide_conserved_regionc, polypeptide_structural_regionc, polypeptide_variation_sitec, protease_sitec, protein_stability_elementc

polypeptide_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001068

Range.
has super-classes
polypeptide_conserved_regionc

polypeptide_secondary_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001078

Biosapien term was secondary_structure.
has super-classes
polypeptide_structural_regionc
has sub-classes
alpha_beta_motifc, asx_motifc, beta_bulgec, beta_bulge_loopc, beta_strandc, catmat_left_handed_fourc, catmat_left_handed_threec, catmat_right_handed_fourc, catmat_right_handed_threec, peptide_coilc, peptide_helixc, polypeptide_nest_motifc, polypeptide_turn_motifc, schellmann_loopc, serine_threonine_motifc, serine_threonine_staple_motifc

polypeptide_sequence_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001603

has super-classes
translational_product_structure_variantc
has sub-classes
amino_acid_deletionc, amino_acid_insertionc, amino_acid_substitutionc, elongated_polypeptidec, polypeptide_fusionc, polypeptide_truncationc

polypeptide_sequencing_informationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001082

Range.
has super-classes
remarkc
has sub-classes
non_adjacent_residuesc, non_terminal_residuec, sequence_conflictc, sequence_uncertaintyc

polypeptide_structural_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001079

has super-classes
polypeptide_structural_regionc
has sub-classes
coiled_coilc, helix_turn_helixc

polypeptide_structural_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001070

Range.
has super-classes
polypeptide_regionc
has sub-classes
extramembrane_polypeptide_regionc, intramembrane_polypeptide_regionc, intrinsically_unstructured_polypeptide_regionc, membrane_structurec, polypeptide_domainc, polypeptide_secondary_structurec, polypeptide_structural_motifc

polypeptide_truncationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001617

has super-classes
polypeptide_sequence_variantc

polypeptide_tungsten_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001102

has super-classes
polypeptide_metal_contactc

polypeptide_turn_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001128

Range.
has super-classes
polypeptide_secondary_structurec
has sub-classes
asx_turnc, beta_turnc, gamma_turnc, serine_threonine_turnc

polypeptide_variation_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001146

For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
has super-classes
polypeptide_regionc
has sub-classes
alternate_sequence_sitec, mutated_variant_sitec, natural_variant_sitec

polypeptide_zinc_ion_contact_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001103

has super-classes
polypeptide_metal_contactc

polyploidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001254

has super-classes
chromosome_number_variationc
has sub-classes
allopolyploidc, autopolyploidc

polypyrimidine_tractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000612

has super-classes
spliceosomal_intron_regionc

population_specific_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001780

has super-classes
variant_originc

positional_candidate_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001868

Requested by Bayer Cropscience December, 2011.
has super-classes
candidate_genec

positive_sense_ssRNA_viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001201

has super-classes
ss_RNA_viral_sequencec

positively_autoregulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000475

has super-classes
transcriptionally_inducedc
autoregulatedc

positively_autoregulated_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000892

is equivalent to
genec and (has_qualityop some positively_autoregulatedc)
has super-classes
genec
has_qualityop some positively_autoregulatedc

possible_assembly_errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000702

has super-classes
sequence_differencec

possible_base_call_errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000701

has super-classes
sequence_differencec

post_translationally_modified_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001089

Discrete.
has super-classes
biochemical_region_of_peptidec
has sub-classes
histone_modificationc, phosphorylation_sitec

post_translationally_regulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000130

has super-classes
regulatedc
has sub-classes
post_translationally_regulated_by_protein_modificationc, post_translationally_regulated_by_protein_stabilityc

post_translationally_regulated_by_protein_modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000469

has super-classes
post_translationally_regulatedc

post_translationally_regulated_by_protein_stabilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000467

has super-classes
post_translationally_regulatedc

post_translationally_regulated_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000890

is equivalent to
genec and (has_qualityop some post_translationally_regulatedc)
has super-classes
genec
has_qualityop some post_translationally_regulatedc

pre_edited_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000932

has super-classes
protein_coding_primary_transcriptc

pre_edited_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000583

has super-classes
edited_transcript_featurec

pre_miRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001244

has super-classes
miRNA_primary_transcript_regionc

predictedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000732

has super-classes
statusc
has sub-classes
orphanc, predicted_by_ab_initio_computationc, supported_by_sequence_similarityc

predicted_ab_initio_computationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000310

predicted_by_ab_initio_computationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000911

has super-classes
predictedc

predicted_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000996

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is equivalent to
genec and (has_qualityop some predictedc)
has super-classes
genec
has_qualityop some predictedc

predicted_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002138

has super-classes
transcriptc
has sub-classes
unconfirmed_transcriptc

presence_absence_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002210

Requested by Bayer Crop Science, March 2018
has super-classes
copy_number_variationc

primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000185

has super-classes
transcriptc
has sub-classes
antisense_primary_transcriptc, capped_primary_transcriptc, mini_exon_donor_RNAc, monocistronic_primary_transcriptc, nc_primary_transcriptc, polycistronic_primary_transcriptc, protein_coding_primary_transcriptc, pseudogenic_transcript_with_retained_intronc, regional_centromere_outer_repeat_transcriptc

primary_transcript_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000144

primary_transcript_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000835

This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
has super-classes
transcript_regionc
part_ofop some primary_transcriptc
has sub-classes
TSSc, clipc, intronc, intron_domainc, miRNA_primary_transcript_regionc, outronc, rRNA_primary_transcript_regionc, splice_regionc, splice_sitec, spliced_leader_RNAc, spliceosomal_intron_regionc, transcription_end_sitec

primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000112

has super-classes
ss_oligoc
has sub-classes
ASPE_primerc, dCAPS_primerc, forward_primerc, reverse_primerc, sequencing_primerc

primer_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005850

has super-classes
nucleotide_binding_sitec
part_ofop some LTR_retrotransposonc

primer_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001472

has super-classes
nucleotide_matchc

priRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002022

has super-classes
ncRNAc

probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000051

has super-classes
oligoc
has sub-classes
microarray_oligoc, smFISH_probec

processedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000900

processed_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000043

Please not the synonym R psi M uses the spelled out form of the greek letter.
has super-classes
pseudogenec
has sub-classes
transcribed_processed_pseudogenec, translated_processed_pseudogenec

processed_pseudogenic_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002193

has super-classes
pseudogenic_rRNAc

processed_pseudogenic_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002197

has super-classes
pseudogenic_tRNAc

processed_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001503

Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
has super-classes
transcriptc
has sub-classes
pseudogene_processed_transcriptc

processed_transcript_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000082

prokaryotic_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002222

has super-classes
promoterc
has sub-classes
bacterial_RNApol_promoterc

prolinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001439

A place holder for a cross product with chebi.
has super-classes
amino_acidc

proline_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000225

has super-classes
tRNA_primary_transcriptc

prolyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000268

has super-classes
tRNAc
derives_fromop some proline_tRNA_primary_transcriptc

promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000167

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter.
has super-classes
gene_component_regionc
transcriptional_cis_regulatory_regionc
has sub-classes
bidirectional_promoterc, constitutive_promoterc, cryptic_promoterc, eukaryotic_promoterc, inducible_promoterc, prokaryotic_promoterc, viral_promoterc

promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001659

Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
has super-classes
DNA_motifc
overlapsop some TF_binding_sitec
part_ofop some promoterc
has sub-classes
AP_1_binding_sitec, Ace2_UASc, CArG_boxc, CCAAT_motifc, CDRE_motifc, CREc, CSL_response_elementc, CTCF_binding_sitec, CuREc, DMv1_motifc, DMv2_motifc, DMv3_motifc, DMv4_motifc, DMv5_motifc, DPE1_motifc, DREc, FLEX_elementc, GC_rich_promoter_regionc, HSEc, MCBc, NDM2_motifc, NDM3_motifc, PCBc, Pho7_binding_sitec, STREP_motifc, TCS_elementc, TR_boxc, core_promoter_elementc, forkhead_motifc, homol_E_boxc, mating_type_M_boxc, pheromone_response_elementc, regulatory_promoter_elementc, sterol_regulatory_elementc, zinc_repressed_elementc

promoter_flanking_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001952

has super-classes
transcriptional_cis_regulatory_regionc

promoter_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000832

This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.

promoter_targeting_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001058

Obsoleted Jan 21, 2021 by Dave Sant. GREEKC consortium individuals pointed out that this did not fit with the other child terms of transcriptional_cis_regulatory_region (SO:0001055), which are currently promoter, CRM and promoter flanking region. No comments about when this term was created exist, no references are listed. GREEKC members assume that this was previously under enhansosome (SO:0001057), which was probably created along with this term but has since been obsoleted. This term can be resurrected as non-obsolete if we can find a reference publication and/or change the name to a term that is commonly used in the field.
has super-classes
transcriptional_cis_regulatory_regionc

promoter_trap_constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001478

has super-classes
engineered_plasmidc

propeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001062

Range.
has super-classes
cleaved_peptide_regionc
derives_fromop some propeptide_region_of_CDSc

propeptide_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001061

Discrete.
has super-classes
cleaved_peptide_regionc
part_ofop some propeptidec

propeptide_region_of_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002250

Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
has super-classes
CDS_regionc

prophagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001006

has super-classes
proviral_regionc

proplastid_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000096

is equivalent to
plastid_genec and (has_originop some proplastid_sequencec)
has super-classes
plastid_genec
has_originop some proplastid_sequencec

proplastid_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000748

has super-classes
plastid_sequencec

protease_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001956

has super-classes
polypeptide_regionc

protein_altering_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001818

has super-classes
coding_sequence_variantc
has sub-classes
frameshift_variantc, inframe_variantc

protein_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000410

See GO:0042277 : peptide binding.
has super-classes
binding_sitec
has sub-classes
nucleotide_to_protein_binding_sitec, protein_protein_contactc

protein_codingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000010

has super-classes
gene_attributec
has sub-classes
intein_containingc

protein_coding_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001217

is equivalent to
genec and (has_qualityop some protein_codingc)
has super-classes
genec
has_qualityop some protein_codingc
has sub-classes
gene_with_edited_transcriptc, gene_with_mRNA_with_frameshiftc, gene_with_polyadenylated_mRNAc, gene_with_recoded_mRNAc

protein_coding_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000120

May contain introns.
has super-classes
primary_transcriptc
has sub-classes
NMD_transcriptc, coding_transcript_with_retained_intronc, pre_edited_mRNAc

protein_hmm_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001831

has super-classes
protein_matchc

protein_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000349

has super-classes
matchc
has sub-classes
protein_hmm_matchc

protein_protein_contactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001093

has super-classes
protein_binding_sitec
molecular_contact_regionc
has sub-classes
DDB_boxc, PIP_boxc, SUMO_interaction_motifc

protein_stability_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001955

has super-classes
polypeptide_regionc

proviral_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000099

is equivalent to
genec and (has_originop some proviral_locationc)
has super-classes
genec
has_originop some proviral_locationc
has sub-classes
endogenous_retroviral_genec

proviral_locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000751

has super-classes
sequence_locationc
has sub-classes
endogenous_retroviral_sequencec

proviral_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000113

has super-classes
integrated_mobile_genetic_elementc
has sub-classes
prophagec

proximal_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001668

has super-classes
regulatory_promoter_elementc

PSE_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000017

has super-classes
DNA_motifc
part_ofop some promoterc

pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000336

has super-classes
biological_regionc
non_functional_homolog_ofop some genec
has sub-classes
non_processed_pseudogenec, polymorphic_pseudogenec, processed_pseudogenec, transposable_element_pseudogenec, vertebrate_immune_system_pseudogenec

pseudogene_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000042

pseudogene_by_unequal_crossing_overc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000044

has super-classes
non_processed_pseudogenec

pseudogene_processed_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002111

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
processed_transcriptc
has sub-classes
polymorphic_pseudogene_processed_transcriptc

pseudogenic_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002087

has super-classes
pseudogenic_regionc
part_ofop some pseudogenic_transcriptc

pseudogenic_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000507

This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
has super-classes
pseudogenic_regionc
non_functional_homolog_ofop some exonc
part_ofop some pseudogenic_transcriptc

pseudogenic_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001741

has super-classes
gene_segmentc

pseudogenic_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000462

has super-classes
biological_regionc
has sub-classes
decayed_exonc, pseudogenic_CDSc, pseudogenic_exonc, pseudogenic_transcriptc

pseudogenic_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000777

Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
has super-classes
pseudogenic_transcriptc
has sub-classes
allelic_pseudogenic_rRNAc, processed_pseudogenic_rRNAc, unitary_pseudogenic_rRNAc, unprocessed_pseudogenic_rRNAc

pseudogenic_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000516

This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
has super-classes
pseudogenic_regionc
part_ofop some pseudogenec
non_functional_homolog_ofop some transcriptc
has sub-classes
pseudogenic_rRNAc, pseudogenic_tRNAc

pseudogenic_transcript_with_retained_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002115

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
has super-classes
primary_transcriptc

pseudogenic_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000778

Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
has super-classes
pseudogenic_transcriptc
has sub-classes
allelic_pseudogenic_tRNAc, processed_pseudogenic_tRNAc, unitary_pseudogenic_tRNAc, unprocessed_pseudogenic_tRNAc

pseudoknotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000591

has super-classes
sequence_secondary_structurec
has sub-classes
H_pseudoknotc, recoding_pseudoknotc

pseudouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001229

The free molecule is CHEBI:17802.
has super-classes
modified_uridinec

pseudouridylation_guide_snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001187

Has RNA pseudouridylation guide activity (GO:0030558).
has super-classes
H_ACA_box_snoRNAc

pumilio_response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002234

Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455)
has super-classes
UTR_regionc
part_ofop some three_prime_UTRc

purine_to_pyrimidine_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000023

has super-classes
transversionc
has sub-classes
A_to_C_transversionc, A_to_T_transversionc, G_to_C_transversionc, G_to_T_transversionc

purine_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000014

has super-classes
transitionc
has sub-classes
A_to_G_transitionc, G_to_A_transitionc

pyrimidine_to_purine_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000018

has super-classes
transversionc
has sub-classes
C_to_A_transversionc, C_to_G_transversionc, T_to_A_transversionc, T_to_G_transversionc

pyrimidine_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000010

has super-classes
transitionc
has sub-classes
C_to_T_transitionc, T_to_C_transitionc

pyrosequenced_readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001424

An example is a read produced by Roche 454 technology.
has super-classes
readc

pyrrolysinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001456

A place holder for a cross product with chebi.
has super-classes
amino_acidc

pyrrolysine_lossc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002010

Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
has super-classes
rare_amino_acid_variantc

pyrrolysine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001178

has super-classes
tRNA_primary_transcriptc

pyrrolysyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000766

has super-classes
tRNAc
derives_fromop some pyrrolysine_tRNA_primary_transcriptc

QTLc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000771

Added in respose to request by Simon Twigger November 14th 2005.
has super-classes
biological_regionc

quality_valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001686

has super-classes
experimental_feature_attributec

quantitative_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001774

has super-classes
variant_phenotypec

queuosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001317

has super-classes
seven_deazaguanosinec

R2_LINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002269

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LINE_elementc

R_five_prime_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000427

has super-classes
R_LTR_regionc
five_prime_LTR_componentc

R_GNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001194

Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
has super-classes
GNAc

R_GNA_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001195

is equivalent to
GNA_oligoc and (has_qualityop some R_GNAc)
has super-classes
GNA_oligoc
has_qualityop some R_GNAc

R_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000423

has super-classes
LTR_componentc
has sub-classes
R_five_prime_LTR_regionc

R_three_prime_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000430

has super-classes
three_prime_LTR_componentc

random_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000449

has super-classes
synthetic_sequencec

RAPDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001481

has super-classes
PCR_productc

rare_amino_acid_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002008

Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
has super-classes
non_conservative_missense_variantc
has sub-classes
pyrrolysine_lossc, selenocysteine_lossc

rare_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001765

has super-classes
variant_frequencyc

rasiRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000454

has super-classes
ncRNAc

rate_of_transcription_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001550

has super-classes
transcription_variantc
has sub-classes
decreased_transcription_rate_variantc, increased_transcription_rate_variantc

rDNA_intergenic_spacer_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001860

Page 208 of ISBN:978-0199638901
has super-classes
DNA_motifc

rDNA_replication_fork_barrierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001914

Requested by Midori - June 2012.
has super-classes
DNA_motifc

readc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000150

has super-classes
assembly_componentc
part_ofop some contigc
has sub-classes
BAC_endc, PAC_endc, YAC_endc, chloroplast_DNA_readc, clone_endc, contig_readc, dye_terminator_readc, genomic_DNA_readc, ligation_based_readc, mRNA_readc, mitochondrial_DNA_readc, polymerase_synthesis_readc, pyrosequenced_readc, read_pairc

read_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000007

has super-classes
readc
part_ofop some contigc
part_ofop some paired_end_fragmentc

reading_framec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000717

This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
has super-classes
experimental_featurec
has sub-classes
ORFc, blocked_reading_framec, disabled_reading_framec

reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000695

Requested by Lynn Crosby, jan 2006.
has super-classes
biomaterial_regionc
has sub-classes
PCR_productc, clonec, clone_insertc, cloned_regionc, databank_entryc, oligoc, rescue_regionc

reagent_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000786

Added jan 2006 by KE.

rearranged_at_DNA_levelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000904

has super-classes
epigenetically_modifiedc

rearrangement_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001872

NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
has super-classes
biological_regionc
structural_alterationc

reciprocalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001521

has super-classes
translocaton_attributec

reciprocal_chromosomal_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000048

has super-classes
chromosomal_translocationc

recodedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000881

has super-classes
mRNA_attributec
has sub-classes
codon_redefinedc, recoded_by_translational_bypassc, translationally_frameshiftedc

recoded_by_translational_bypassc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000886

has super-classes
recodedc

recoded_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000145

has super-classes
codonc
has sub-classes
stop_codon_read_throughc

recoded_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001261

is equivalent to
mRNAc and (has_qualityop some recodedc)
has super-classes
mRNAc
has_qualityop some recodedc
has sub-classes
mRNA_recoded_by_codon_redefinitionc, mRNA_recoded_by_translational_bypassc

recoding_pseudoknotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000545

has super-classes
pseudoknotc
part_ofop some recoding_stimulatory_regionc

recoding_stimulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001268

has super-classes
mRNA_regionc
has sub-classes
SECIS_elementc, five_prime_recoding_sitec, internal_Shine_Dalgarno_sequencec, stop_codon_signalc, three_prime_recoding_sitec

recombination_enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002059

has super-classes
recombination_regulatory_regionc

recombination_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000298

has super-classes
biological_regionc
has sub-classes
haplotype_blockc, iDNAc, meiotic_recombination_regionc, mitotic_recombination_regionc, recombination_hotspotc, sequence_rearrangement_featurec

recombination_feature_of_rearranged_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000300

has super-classes
specific_recombination_sitec
has sub-classes
vertebrate_immune_system_gene_recombination_featurec

recombination_hotspotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000339

has super-classes
recombination_featurec
has sub-classes
non_allelic_homologous_recombination_regionc

recombination_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001681

has super-classes
regulatory_regionc
has sub-classes
recombination_enhancerc

recombination_signal_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001532

has super-classes
specific_recombination_sitec

recombinationally_inverted_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000373

is equivalent to
recombinationally_rearranged_genec and (has_qualityop some inversionc)
has super-classes
recombinationally_rearranged_genec
has_qualityop some inversionc

recombinationally_rearrangedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000940

has super-classes
feature_attributec

recombinationally_rearranged_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000456

is equivalent to
genec and (has_qualityop some recombinationally_rearrangedc)
has super-classes
genec
has_qualityop some recombinationally_rearrangedc
has sub-classes
recombinationally_inverted_genec, recombinationally_rearranged_vertebrate_immune_system_genec

recombinationally_rearranged_vertebrate_immune_system_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000941

has super-classes
recombinationally_rearranged_genec

recursive_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000998

has super-classes
cis_splice_sitec

redundant_inserted_stop_gainedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002214

has super-classes
nonsynonymous_variantc

ref_miRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002166

has super-classes
miRNAc

reference_genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001505

has super-classes
genomec

regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000001

has super-classes
sequence_featurec
has sub-classes
biological_regionc, biomaterial_regionc, experimental_featurec, topologically_defined_regionc

regional_centromerec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001795

has super-classes
centromerec

regional_centromere_central_corec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001796

has super-classes
conserved_regionc
part_ofop some regional_centromerec

regional_centromere_inner_repeat_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001798

has super-classes
centromeric_repeatc
part_ofop some regional_centromerec
part_ofop some regional_centromere_central_corec

regional_centromere_outer_repeat_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001799

has super-classes
centromeric_repeatc
part_ofop some regional_centromerec

regional_centromere_outer_repeat_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001905

is equivalent to
primary_transcriptc and (derives_fromop some regional_centromere_outer_repeat_regionc)
has super-classes
primary_transcriptc
derives_fromop some regional_centromere_outer_repeat_regionc

regulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000119

has super-classes
gene_attributec
has sub-classes
genomically_imprintedc, post_translationally_regulatedc, transcriptionally_regulatedc, translationally_regulatedc

regulatory_promoter_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001678

has super-classes
promoter_elementc
has sub-classes
G_boxc, I-boxc, L_boxc, distal_promoter_elementc, proximal_promoter_elementc

regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005836

has super-classes
gene_member_regionc
has sub-classes
epigenetically_modified_regionc, inert_DNA_spacerc, recombination_regulatory_regionc, replication_regulatory_regionc, transcriptional_cis_regulatory_regionc, translation_regulatory_regionc

regulatory_region_ablationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001894

Created in conjunction with the EBI.
has super-classes
feature_ablationc
has sub-classes
TFBS_ablationc

regulatory_region_amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001891

Created in conjunction with the EBI.
has super-classes
feature_amplificationc
has sub-classes
TFBS_amplificationc

regulatory_region_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001887

Created in conjunction with the EBI.
has super-classes
feature_fusionc
has sub-classes
TFBS_fusionc

regulatory_region_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001884

Created in conjunction with the EBI.
has super-classes
feature_translocationc
has sub-classes
TFBS_translocationc

regulatory_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001566

EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
has super-classes
feature_variantc
has sub-classes
TF_binding_site_variantc

regulonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001284

Definition updated with Mejia-Almonte et.al PMID:32665585 on Aug 5, 2020. Added relationship has_part SO:0002300
has super-classes
gene_groupc
has_partop some unit_of_gene_expressionc
has sub-classes
complex_regulonc, simple_regulonc

remarkc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000700

has super-classes
experimental_featurec
has sub-classes
experimental_result_regionc, polypeptide_sequencing_informationc, sequence_differencec

repeat_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000840

A manufactured to group the parts of repeats, to give them an is_a path back to the root.
has super-classes
topologically_defined_regionc
has sub-classes
LTR_componentc, non_LTR_retrotransposon_polymeric_tractc, repeat_fragmentc, transposon_fragmentc

repeat_familyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000187

repeat_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001050

Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
has super-classes
repeat_componentc
part_ofop some nested_repeatc

repeat_instability_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002202

has super-classes
tandem_repeatc

repeat_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000657

has super-classes
biological_regionc
has_partop some repeat_unitc
has sub-classes
X_element_combinatorial_repeatc, Y_prime_elementc, centromeric_repeatc, direct_repeatc, dispersed_repeatc, engineered_foreign_repetitive_elementc, flanking_repeatc, inverted_repeatc, knobc, long_terminal_repeatc, nested_repeatc, non_LTR_retrotransposon_polymeric_tractc, tandem_repeatc, telomeric_repeatc, terminal_repeatc

repeat_unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000726

Added to comply with the feature table. A single repeat.
has super-classes
biological_regionc

repetitive_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000292

replication_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001682

has super-classes
regulatory_regionc

replication_start_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002203

has super-classes
origin_of_replicationc

repliconc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001235

has super-classes
biological_regionc
has sub-classes
chromosomec, maxicirclec, minicirclec, plasmidc, vector_repliconc, viral_sequencec

rescuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000814

has super-classes
feature_attributec

rescue_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000816

is equivalent to
genec and (has_qualityop some rescuec)
has super-classes
genec
has_qualityop some rescuec
has sub-classes
wild_type_rescue_genec

rescue_mini_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000795

is equivalent to
mini_genec and (has_qualityop some rescuec)
has super-classes
mini_genec
has_qualityop some rescuec

rescue_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000411

is equivalent to
reagentc and (has_qualityop some rescuec)
has super-classes
reagentc
has_qualityop some rescuec
has sub-classes
engineered_rescue_regionc

resolution_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000947

has super-classes
site_specific_recombination_target_regionc
has sub-classes
dif_sitec, loxP_sitec

response_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002205

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc

restriction_enzyme_assembly_scarc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001953

has super-classes
restriction_enzyme_regionc

restriction_enzyme_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000061

A region of a molecule that binds to a restriction enzyme.
has super-classes
nuclease_binding_sitec

restriction_enzyme_cleavage_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001688

has super-classes
nucleotide_cleavage_sitec
has sub-classes
blunt_end_restriction_enzyme_cleavage_junctionc, single_strand_restriction_enzyme_cleavage_sitec

restriction_enzyme_cut_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000168

restriction_enzyme_five_prime_single_strand_overhangc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001932

has super-classes
restriction_enzyme_single_strand_overhangc

restriction_enzyme_recognition_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001687

has super-classes
restriction_enzyme_regionc
has sub-classes
blunt_end_restriction_enzyme_cleavage_sitec, sticky_end_restriction_enzyme_cleavage_sitec

restriction_enzyme_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001954

Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
has super-classes
biological_regionc
has sub-classes
restriction_enzyme_assembly_scarc, restriction_enzyme_recognition_sitec, restriction_enzyme_single_strand_overhangc

restriction_enzyme_single_strand_overhangc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001695

has super-classes
restriction_enzyme_regionc
part_ofop some sticky_end_restriction_enzyme_cleavage_sitec
has sub-classes
restriction_enzyme_five_prime_single_strand_overhangc, restriction_enzyme_three_prime_single_strand_overhangc

restriction_enzyme_three_prime_single_strand_overhangc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001933

has super-classes
restriction_enzyme_single_strand_overhangc

restriction_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000412

has super-classes
assembly_componentc
has sub-classes
RFLP_fragmentc

retinoic_acid_responsive_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001653

has super-classes
TF_binding_sitec

retrogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001219

is equivalent to
genec and (has_qualityop some retrotransposedc)
has super-classes
genec
has_qualityop some retrotransposedc

retronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001275

has super-classes
biological_regionc

retrotransposedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000569

GO:0003964 RNA-directed DNA polymerase activity.
has super-classes
feature_attributec

retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000180

has super-classes
transposable_elementc
has sub-classes
LTR_retrotransposonc, non_LTR_retrotransposonc

Retrovirus_LTR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002267

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LTR_retrotransposonc

reversec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001031

has super-classes
direction_attributec

reverse_Hoogsteen_base_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000501

has super-classes
base_pairc

reverse_primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000132

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is equivalent to
primerc and (has_qualityop some reversec)
has super-classes
primerc
has_qualityop some reversec

RFLP_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000193

has super-classes
restriction_fragmentc

RH_mapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001252

has super-classes
fragment_assemblyc
has_partop some STSc

rho_dependent_bacterial_terminatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000981

has super-classes
bacterial_terminatorc

rho_independent_bacterial_terminatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000982

has super-classes
bacterial_terminatorc

ribonuclease_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001977

has super-classes
transcript_regionc

ribosome_entry_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000139

has super-classes
mRNA_regionc
part_ofop some five_prime_UTRc
has sub-classes
Shine_Dalgarno_sequencec, internal_ribosome_entry_sitec, kozak_sequencec

riboswitchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000035

has super-classes
mRNA_regionc
part_ofop some mRNAc

ribothymidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001232

The free molecule is CHEBI:30832.
has super-classes
modified_RNA_base_featurec

ribozymec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000374

is equivalent to
enzymatic_RNAc and (has_qualityop some ribozymicc)
has super-classes
enzymatic_RNAc
has_qualityop some ribozymicc
has sub-classes
self_cleaving_ribozymec

ribozyme_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002181

has super-classes
enzymatic_RNA_genec

ribozymicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001186

Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
has super-classes
enzymaticc

right_handed_peptide_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001116

has super-classes
peptide_helixc
has sub-classes
alpha_helixc, pi_helixc, three_ten_helixc

ring_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000045

is equivalent to
intrachromosomal_mutationc and (has_qualityop some circularc)
has super-classes
intrachromosomal_mutationc
has_qualityop some circularc
has sub-classes
free_ring_duplicationc, inverted_ring_chromosomec

RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000356

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
nucleic_acidc

RNA_6Sc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000376

has super-classes
small_regulatory_ncRNAc

RNA_7SKc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002340

Added as a request from FlyBase. See GitHub Issue #512
has super-classes
ncRNAc

RNA_7SK_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002341

Added as a request from FlyBase. See GitHub Issue #512
has super-classes
ncRNA_genec

RNA_aptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000033

has super-classes
aptamerc

RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000961

is equivalent to
chromosomec and (has_qualityop some RNAc)
has super-classes
chromosomec
has_qualityop some RNAc
has sub-classes
double_stranded_RNA_chromosomec, single_stranded_RNA_chromosomec

RNA_hook_turnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000027

has super-classes
RNA_junction_loopc

RNA_internal_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000020

has super-classes
RNA_motifc
has sub-classes
asymmetric_RNA_internal_loopc, symmetric_RNA_internal_loopc

RNA_junction_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000026

has super-classes
RNA_motifc
has sub-classes
RNA_hook_turnc

RNA_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000715

has super-classes
nucleotide_motifc
has sub-classes
A_minor_RNA_motifc, RNA_internal_loopc, RNA_junction_loopc, RNA_stability_elementc, hammerhead_ribozymec

RNA_polymerase_II_TATA_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001661

has super-classes
TATA_boxc
part_ofop some RNApol_II_core_promoterc

RNA_polymerase_III_TATA_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001662

has super-classes
TATA_boxc
part_ofop some RNApol_III_promoterc

RNA_polymerase_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001203

Term merged with promoter SO:0000167 in August 2020 as part of GREEKC initiative. See GitHub Issue 492 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/492)

RNA_replication_modec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000972

This has been obsoleted as it represents a process. replaced_by: GO:0034961.

RNA_sequence_secondary_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000122

has super-classes
sequence_secondary_structurec
has sub-classes
stem_loopc, stem_loop_regionc

RNA_stability_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001957

RNA_stability_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001979

has super-classes
RNA_motifc
has sub-classes
UNAAAC_motifc

RNA_thermometerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002168

has super-classes
mRNA_regionc
part_ofop some mRNAc

RNAi_reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000337

has super-classes
ds_oligoc

RNApol_I_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000169

parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
has super-classes
eukaryotic_promoterc

RNApol_II_core_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001669

has super-classes
RNApol_II_promoterc

RNApol_II_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000170

parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
has super-classes
eukaryotic_promoterc
has sub-classes
RNApol_II_core_promoterc

RNApol_II_promoter_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000844

This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.

RNApol_III_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000171

parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
has super-classes
eukaryotic_promoterc
has sub-classes
RNApol_III_promoter_type_1c, RNApol_III_promoter_type_2c, RNApol_III_promoter_type_3c

RNApol_III_promoter_type_1c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000617

has super-classes
RNApol_III_promoterc

RNApol_III_promoter_type_1_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000845

This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.

RNApol_III_promoter_type_2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000618

has super-classes
RNApol_III_promoterc

RNApol_III_promoter_type_2_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000846

This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.

RNApol_III_promoter_type_3c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000621

has super-classes
RNApol_III_promoterc

RNase_MRP_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000385

has super-classes
ncRNAc

RNase_MRP_RNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001640

has super-classes
ncRNA_genec

RNase_P_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000386

has super-classes
ncRNAc

RNase_P_RNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001639

has super-classes
ncRNA_genec

Robertsonian_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000043

has super-classes
chromosomal_translocationc

rolling_circlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000969

This has been obsoleted as it represents a process. replaced_by: GO:0070581.

RprA_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000387

has super-classes
small_regulatory_ncRNAc

RR_tractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000435

has super-classes
conserved_regionc
part_ofop some LTR_retrotransposonc

RRE_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000388

has super-classes
small_regulatory_ncRNAc

rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000252

Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493
has super-classes
ncRNAc
derives_fromop some rRNA_primary_transcriptc
has sub-classes
cytosolic_rRNAc, mt_rRNAc, plastid_rRNAc

rRNA_16S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002237

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_16S_rRNAc

rRNA_18S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002236

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_18S_rRNAc

rRNA_21Sc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001171

This term has been merged into mt_LSU_rRNA (SO:0002345) as part of reorganization of rRNA child terms 10 June 2021. Requested by EBI. See GitHub Issue #493.

rRNA_21S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002241

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472) Removed relationship derives_from SO:0001171 on 10 June 2021 when SO:0001171 rRNA_21S was obsoleted into SO:0002345 mt_LSU_rRNA. See GitHub Issue #493.
has super-classes
rRNA_genec

rRNA_23S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002243

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_23S_rRNAc

rRNA_25S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002242

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_25S_rRNAc

rRNA_28S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002239

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_28S_rRNAc

rRNA_2S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002336

Added as a request from FlyBase. See GitHub Issue #507
has super-classes
rRNA_genec

rRNA_5_8S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002240

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_5_8S_rRNAc

rRNA_5S_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002238

Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472)
has super-classes
rRNA_genec
derives_fromop some cytosolic_5S_rRNAc

rRNA_cleavage_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005843

has super-classes
ncRNAc
derives_fromop some rRNA_cleavage_snoRNA_primary_transcriptc

rRNA_cleavage_snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000582

has super-classes
snoRNA_primary_transcriptc

rRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000573

has super-classes
non_protein_codingc

rRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001637

has super-classes
ncRNA_genec
has sub-classes
rRNA_16S_genec, rRNA_18S_genec, rRNA_21S_genec, rRNA_23S_genec, rRNA_25S_genec, rRNA_28S_genec, rRNA_2S_genec, rRNA_5S_genec, rRNA_5_8S_genec

rRNA_large_subunit_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000325

has super-classes
rRNA_primary_transcriptc

rRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000209

has super-classes
nc_primary_transcriptc
has sub-classes
rRNA_large_subunit_primary_transcriptc, rRNA_small_subunit_primary_transcriptc

rRNA_primary_transcript_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000838

To allow transcribed_spacer_region to have a path to the root.
has super-classes
primary_transcript_regionc
part_ofop some rRNA_primary_transcriptc
has sub-classes
transcribed_spacer_regionc

rRNA_small_subunit_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000255

has super-classes
rRNA_primary_transcriptc

RSTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001467

has super-classes
ESTc
has sub-classes
five_prime_RSTc, three_prime_RSTc

RST_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001471

has super-classes
expressed_sequence_matchc

RTE_LINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002270

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
LINE_elementc

s o 0000019c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000019

s o 0000358c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000358

s o 0000648c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000648

s o 0000649c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000649

s o 0000826c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000826

s o 0000827c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000827

s o 0000974c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000974

s o 0001065c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001065

s o 0001069c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001069

s o 0001242c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001242

s o 0001270c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001270

s o 0001430c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001430

s o 0001581c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001581

s o 0001584c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001584

s o 0001588c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001588

s o 0001625c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001625

s o 0001651c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001651

s o 0001652c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001652

s o 0001783c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001783

s o 0001900c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001900

s o 0001903c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001903

s o 0002000c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002000

s o 0005839c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005839

s o 0100042c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0100042

s o 1000004c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000004

s o 1000007c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000007

s o 1000033c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000033

s o 1000034c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000034

s o 1000090c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000090

s o 1000091c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000091

s o 1000113c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000113

s o 1000114c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000114

s o 1000146c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000146

s o 1000177c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000177

s o 1000179c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000179

S_GNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001196

Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
has super-classes
GNAc

S_GNA_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001197

is equivalent to
GNA_oligoc and (has_qualityop some S_GNAc)
has super-classes
GNA_oligoc
has_qualityop some S_GNAc

S_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001836

has super-classes
vertebrate_immune_system_gene_recombination_featurec

SAGE_tagc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000326

has super-classes
tagc

Sap1_recognition_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001864

has super-classes
DNA_motifc

sarcin_like_RNA_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000024

has super-classes
asymmetric_RNA_internal_loopc

satellite_DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000005

has super-classes
tandem_repeatc
has sub-classes
microsatellitec, minisatellitec

scaRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002095

Moved from is_a ncRNA (SO:0000655) to is_a snoRNA (SO:0000275) as per request from FlyBase by Dave Sant 24 April 2021. See GitHub Issue #509.
has super-classes
snoRNAc

scaRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002339

Added as a request from FlyBase. See GitHub Issue #510
has super-classes
snoRNA_genec

schellmann_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001123

has super-classes
polypeptide_secondary_structurec
has sub-classes
schellmann_loop_sevenc, schellmann_loop_sixc

schellmann_loop_sevenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001124

has super-classes
schellmann_loopc

schellmann_loop_sixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001125

has super-classes
schellmann_loopc

scorec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001685

has super-classes
experimental_feature_attributec

scRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000013

has super-classes
ncRNAc
derives_fromop some scRNA_primary_transcriptc

scRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000575

has super-classes
non_protein_codingc

scRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001266

is equivalent to
ncRNA_genec and (has_qualityop some scRNA_encodingc)
has super-classes
ncRNA_genec
has_qualityop some scRNA_encodingc

scRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000012

has super-classes
nc_primary_transcriptc

SECIS_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001274

has super-classes
recoding_stimulatory_regionc

selection_markerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002232

Added as per request by Bryan Bartley GitHub issue #468 and #402 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/468)
has super-classes
genetic_markerc

selenocysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001455

A place holder for a cross product with chebi.
has super-classes
amino_acidc

selenocysteine_lossc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002009

Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
has super-classes
rare_amino_acid_variantc

selenocysteine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005856

has super-classes
tRNA_primary_transcriptc

selenocysteinyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005857

has super-classes
tRNAc
derives_fromop some selenocysteine_tRNA_primary_transcriptc

self_cleaving_ribozymec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002231

Added as per request by John T. Sexton GitHub issue #470 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/470)
is equivalent to
ribozymec and (has_qualityop some ribonuclease_sitec)
has super-classes
ribozymec
has_qualityop some ribonuclease_sitec

sense_intronic_ncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002131

has super-classes
lncRNAc

sense_intronic_ncRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002184

has super-classes
lncRNA_genec

sense_overlap_ncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002132

has super-classes
lncRNAc

sense_overlap_ncRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002183

has super-classes
lncRNA_genec

sequence variant_affecting_transcript_stabilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000082

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001059

Merged with partially characterized change in nucleotide sequence.
has super-classes
sequence_comparisonc
has sub-classes
UPDc, deletionc, delinsc, insertionc, inversionc, sequence_length_alterationc, structural_alterationc, substitutionc, unspecified_indelc

sequence_alteration_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002172

has super-classes
sequence_differencec
has sub-classes
deletion_artifactc, indel_artifactc, insertion_artifactc, substitution_artifactc

sequence_assemblyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000353

has super-classes
assemblyc
has sub-classes
contigc, expressed_sequence_assemblyc, golden_pathc, partial_genomic_sequence_assemblyc, tiling_pathc, virtual_sequencec

sequence_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000400

has sub-classes
feature_attributec, polymer_attributec, sequence_locationc, sequence_sourcec, variant_qualityc
is disjoint with
sequence_featurec

sequence_collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001260

has sub-classes
contig_collectionc, genomec, peptide_collectionc, variant_collectionc

sequence_comparisonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002072

has super-classes
sequence_featurec
has sub-classes
no_sequence_alterationc, sequence_alterationc

sequence_conflictc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001085

Discrete.
has super-classes
polypeptide_sequencing_informationc
has sub-classes
contig_collectionc

sequence_differencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000413

has super-classes
remarkc
has sub-classes
assembly_error_correctionc, base_call_error_correctionc, possible_assembly_errorc, possible_base_call_errorc, sequence_alteration_artifactc

sequence_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000110

has sub-classes
junctionc, regionc, sequence_comparisonc
is disjoint with
sequence_attributec

sequence_feature_locating_methodc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000308

sequence_length_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000248

has super-classes
sequence_alterationc
has sub-classes
copy_number_variationc, short_tandem_repeat_variationc, simple_sequence_length_variationc

sequence_length_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002160

has super-classes
structural_variantc
has sub-classes
copy_number_changec, short_tandem_repeat_changec

sequence_locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000735

has super-classes
sequence_attributec
has sub-classes
nuclear_sequencec, organelle_sequencec, plasmid_locationc, proviral_locationc

sequence_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001683

has super-classes
biological_regionc
has sub-classes
nucleotide_motifc

Sequence_Ontologyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000000

sequence_operationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000041

sequence_rearrangement_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000669

has super-classes
recombination_featurec
has sub-classes
chromosome_breakage_sequencec, internal_eliminated_sequencec, macronucleus_destined_segmentc, specific_recombination_sitec

sequence_replication_modec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000968

This has been obsoleted as it represents a process. replaced_by: GO:0034961.

sequence_secondary_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000002

has super-classes
biological_regionc
has sub-classes
DNA_sequence_secondary_structurec, G_quartetc, RNA_sequence_secondary_structurec, base_pairc, pseudoknotc

sequence_sourcec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002206

Terms such as genomic_DNA or mRNA can be used to describe a sequence source.
has super-classes
sequence_attributec

sequence_uncertaintyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001086

has super-classes
polypeptide_sequencing_informationc

sequence_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001060

has sub-classes
functional_effect_variantc, structural_variantc

sequence_variant_affecting_3D_structure_of_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000111

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_copy_numberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001020

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_editingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000075

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_gene_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000180

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_level_of_translational_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000102

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_polyadenylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001432

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_polypeptide_amino_acid_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000105

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_polypeptide_functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000117

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_rate_of_transcriptionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000081

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000053

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_splice_acceptorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000073

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_splice_donorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000072

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_splicingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000071

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_transcript_processingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000070

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_transcript_secondary_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000126

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_transcriptionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000076

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_translational_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000088

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causes_exon_lossc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000184

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causes_intron_gainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000185

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_coding_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000056

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000097

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000096

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000093

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_compensatory_transcript_secondary_structure_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000127

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_complex_3D_structural_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000115

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_complex_change_of_translational_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000092

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_conformational_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000116

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_conservative_amino_acid_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000094

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_conservative_missense_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000060

The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.

sequence_variant_causing_cryptic_splice_acceptor_activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001186

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_cryptic_splice_activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000074

A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.

sequence_variant_causing_cryptic_splice_donor_activationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000186

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_gain_of_function_of_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000125

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_gene_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000181

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_inactive_catalytic_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000120

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_inactive_ligand_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000119

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_initiator_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000055

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_loss_of_function_of_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000118

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_minus_1_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000067

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_minus_2_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000069

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_missense_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000059

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_no_3D_structural_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000112

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.

sequence_variant_causing_no_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000050

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.

sequence_variant_causing_no_change_of_translational_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000089

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.

sequence_variant_causing_non_synonymous_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000058

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_nonconservative_amino_acid_substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000095

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_nonconservative_missense_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000061

The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.

sequence_variant_causing_nonsense_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000062

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_partial_loss_of_function_of_polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000124

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_plus_1_frameshift_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000066

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_plus_2_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000068

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_elongationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000099

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000134

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_localization_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000121

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_post_translational_processing_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000122

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_truncationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000098

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_synonymous_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000057

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_terminator_codon_change_in_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000063

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_decreasing_level_of_translation_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000103

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_decreasing_rate_of_transcriptionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000078

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_decreasing_transcript_stabilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000084

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_effectc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000132

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Updated after discussion with Peter Taschner - Feb 09.

sequence_variant_increasing_level_of_translation_productc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000104

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_increasing_rate_of_transcriptionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000080

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_increasing_transcript_stabilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000083

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_obsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000109

sequence_variation_affecting_coding_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000054

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_level_of_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000085

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_reading_framec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000064

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000049

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_transcript_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000079

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_decreasing_level_of_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000086

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_increasing_level_of_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000087

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequencing_primerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000107

has super-classes
primerc

serinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001444

A place holder for a cross product with chebi.
has super-classes
amino_acidc

serine_threonine_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001126

has super-classes
polypeptide_secondary_structurec

serine_threonine_staple_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001127

has super-classes
polypeptide_secondary_structurec

serine_threonine_turnc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001141

has super-classes
polypeptide_turn_motifc
has sub-classes
st_turn_left_handed_type_onec, st_turn_left_handed_type_twoc, st_turn_right_handed_type_onec, st_turn_right_handed_type_twoc

serine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000226

has super-classes
tRNA_primary_transcriptc

seryl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000269

has super-classes
tRNAc
derives_fromop some serine_tRNA_primary_transcriptc

seven_aminomethyl_seven_deazaguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001322

has super-classes
seven_deazaguanosinec

seven_cyano_seven_deazaguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001321

has super-classes
seven_deazaguanosinec

seven_deazaguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001316

has super-classes
modified_guanosinec
has sub-classes
archaeosinec, epoxyqueuosinec, galactosyl_queuosinec, mannosyl_queuosinec, queuosinec, seven_aminomethyl_seven_deazaguanosinec, seven_cyano_seven_deazaguanosinec

seven_methylguaninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001231

The free molecule is CHEBI:2274.
has super-classes
modified_RNA_base_featurec

seven_methylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001326

has super-classes
modified_guanosinec

sgRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001998

has super-classes
oligoc

shadow_enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001482

has super-classes
enhancerc

Shine_Dalgarno_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000552

Not found in Eukaryotic sequence.
has super-classes
ribosome_entry_sitec

short_tandem_repeat_changec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002161

has super-classes
sequence_length_variantc
has sub-classes
short_tandem_repeat_contractionc, short_tandem_repeat_expansionc

short_tandem_repeat_contractionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002163

has super-classes
short_tandem_repeat_changec

short_tandem_repeat_expansionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002162

has super-classes
short_tandem_repeat_changec
has sub-classes
trinucleotide_repeat_expansionc

short_tandem_repeat_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002096

has super-classes
sequence_length_alterationc

SHP_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002159

has super-classes
polypeptide_conserved_motifc

shRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002031

has super-classes
ncRNAc

shRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002038

has super-classes
nc_primary_transcriptc
has sub-classes
miR_encoding_shRNA_primary_transcriptc

signal_anchorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001809

has super-classes
signal_peptidec

signal_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000418

Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
has super-classes
peptide_localization_signalc
derives_fromop some signal_peptide_region_of_CDSc
part_ofop some propeptidec
has sub-classes
signal_anchorc

signal_peptide_region_of_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002251

Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
has super-classes
CDS_regionc

signaturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001978

Requested by Jackie Quinn for use in synthetic biology.
has super-classes
engineered_regionc

silencedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000893

has super-classes
transcriptionally_repressedc
has sub-classes
silenced_by_DNA_modificationc, silenced_by_RNA_interferencec, silenced_by_histone_modificationc

silenced_by_DNA_methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000895

has super-classes
silenced_by_DNA_modificationc

silenced_by_DNA_modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000894

has super-classes
silencedc
has sub-classes
silenced_by_DNA_methylationc

silenced_by_histone_deacetylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001223

Histone deacetylation is GO:0016573.
has super-classes
silenced_by_histone_modificationc

silenced_by_histone_methylationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001222

Histone methylation is GO:0016571.
has super-classes
silenced_by_histone_modificationc

silenced_by_histone_modificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001221

Histone modification is GO:0016570.
has super-classes
silencedc
has sub-classes
silenced_by_histone_deacetylationc, silenced_by_histone_methylationc

silenced_by_RNA_interferencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001220

RNA interference is GO:0016246.
has super-classes
silencedc

silenced_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000127

is equivalent to
genec and (has_qualityop some silencedc)
has super-classes
genec
has_qualityop some silencedc
has sub-classes
gene_silenced_by_DNA_modificationc, gene_silenced_by_RNA_interferencec, gene_silenced_by_histone_modificationc

silencerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000625

has super-classes
cis_regulatory_modulec
has sub-classes
exonic_splicing_silencerc, intronic_splicing_silencerc

silent_mating_type_cassette_arrayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001984

has super-classes
gene_cassette_arrayc
has sub-classes
Mat2Pc, Mat3Mc

silent_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001017

Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
has super-classes
feature_variantc

simple_operonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002298

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
operonc

simple_regulonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002302

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
regulonc

simple_sequence_length_variationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000207

has super-classes
sequence_length_alterationc

SINE_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000206

has super-classes
non_LTR_retrotransposonc
has sub-classes
5S_SINE_retrotransposonc, 7SL_SINE_retrotransposonc, tRNA_SINE_retrotransposonc

singlec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000984

Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
has super-classes
strand_attributec

single_strand_restriction_enzyme_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001694

has super-classes
restriction_enzyme_cleavage_junctionc
has sub-classes
five_prime_restriction_enzyme_junctionc, three_prime_restriction_enzyme_junctionc

single_stranded_cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000757

has super-classes
cDNAc

single_stranded_DNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000956

is equivalent to
DNA_chromosomec and (has_qualityop some singlec)
has super-classes
DNA_chromosomec
has_qualityop some singlec
has sub-classes
circular_single_stranded_DNA_chromosomec, linear_single_stranded_DNA_chromosomec

single_stranded_RNA_chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000962

is equivalent to
RNA_chromosomec and (has_qualityop some singlec)
has super-classes
RNA_chromosomec
has_qualityop some singlec
has sub-classes
circular_single_stranded_RNA_chromosomec, linear_single_stranded_RNA_chromosomec

siRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000646

has super-classes
small_regulatory_ncRNAc

sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000408

site_specific_recombination_target_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000342

has super-classes
specific_recombination_sitec
has sub-classes
integration_excision_sitec, inversion_sitec, inversion_site_partc, resolution_sitec

six_cutter_restriction_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000249

SL10_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001755

has super-classes
SL2_acceptor_sitec

SL11_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001756

has super-classes
SL2_acceptor_sitec

SL12_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001757

has super-classes
SL2_acceptor_sitec

SL1_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000708

has super-classes
trans_splice_acceptor_sitec

SL2_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000709

has super-classes
trans_splice_acceptor_sitec
has sub-classes
SL10_acceptor_sitec, SL11_acceptor_sitec, SL12_acceptor_sitec, SL3_acceptor_sitec, SL4_acceptor_sitec, SL5_acceptor_sitec, SL6_acceptor_sitec, SL7_acceptor_sitec, SL8_acceptor_sitec, SL9_acceptor_sitec

SL3_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001748

has super-classes
SL2_acceptor_sitec

SL4_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001749

has super-classes
SL2_acceptor_sitec

SL5_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001750

has super-classes
SL2_acceptor_sitec

SL6_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001751

has super-classes
SL2_acceptor_sitec

SL7_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001752

has super-classes
SL2_acceptor_sitec

SL8_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001753

has super-classes
SL2_acceptor_sitec

SL9_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001754

has super-classes
SL2_acceptor_sitec

small_regulatory_ncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000370

has super-classes
sncRNAc
has sub-classes
CsrB_RsmB_RNAc, DsrA_RNAc, OxyS_RNAc, RNA_6Sc, RRE_RNAc, RprA_RNAc, loRc, miRNAc, moRc, piRNAc, siRNAc, spot_42_RNAc, tmRNAc

smFISH_probec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001854

has super-classes
probec

sncRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002247

Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485)
has super-classes
ncRNAc
has sub-classes
small_regulatory_ncRNAc, snRNAc, snoRNAc, tRNAc

sncRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002342

Added as a request from FlyBase to make the ncRNA_gene branch in SO mirror the ncRNA branch. See GitHub Issue #514
has super-classes
ncRNA_genec
has sub-classes
miRNA_genec, piRNA_genec, snRNA_genec, snoRNA_genec, tRNA_genec, tmRNA_genec

snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000275

has super-classes
sncRNAc
derives_fromop some snoRNA_primary_transcriptc
has sub-classes
C_D_box_snoRNAc, H_ACA_box_snoRNAc, scaRNAc

snoRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000578

has super-classes
non_protein_codingc
has sub-classes
C_D_box_snoRNA_encodingc, H_ACA_box_snoRNA_encodingc

snoRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001267

Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
is equivalent to
sncRNA_genec and (has_qualityop some snoRNA_encodingc)
has super-classes
sncRNA_genec
has_qualityop some snoRNA_encodingc
has sub-classes
scaRNA_genec

snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000232

This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520).
has super-classes
nc_primary_transcriptc
has sub-classes
C_D_box_snoRNA_primary_transcriptc, H_ACA_box_snoRNA_primary_transcriptc, U14_snoRNA_primary_transcriptc, methylation_guide_snoRNA_primary_transcriptc, miR_encoding_snoRNA_primary_transcriptc, rRNA_cleavage_snoRNA_primary_transcriptc

SNPc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000694

has super-classes
SNVc

snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000274

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
sncRNAc
derives_fromop some snRNA_primary_transcriptc
has sub-classes
U11_snRNAc, U12_snRNAc, U1_snRNAc, U2_snRNAc, U4_snRNAc, U4atac_snRNAc, U5_snRNAc, U6_snRNAc, U6atac_snRNAc, U7_snRNAc

snRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000623

has super-classes
non_protein_codingc

snRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001268

Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
has super-classes
sncRNA_genec

snRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000231

has super-classes
nc_primary_transcriptc

SNVc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001483

has super-classes
substitutionc
has sub-classes
SNPc, point_mutationc, transitionc, transversionc

SNV_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002178

has super-classes
substitution_artifactc

solo_LTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001003

Requested by Hadi Quesneville January 2007.
has super-classes
long_terminal_repeatc

somatic_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001777

has super-classes
variant_originc

sonicate_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001253

has super-classes
assembly_componentc

sORFc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002028

has super-classes
ORFc

SP6_RNA_Polymerase_Promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001205

has super-classes
Phage_RNA_Polymerase_Promoterc

specific_recombination_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000299

has super-classes
sequence_rearrangement_featurec
has sub-classes
recombination_feature_of_rearranged_genec, recombination_signal_sequencec, site_specific_recombination_target_regionc

splice_acceptor_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001574

has super-classes
splice_site_variantc
has sub-classes
splice_acceptor_variant_NMD_escapingc, splice_acceptor_variant_NMD_triggeringc

splice_acceptor_variant_NMD_escapingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002328

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
splice_acceptor_variantc
NMD_escaping_variantc

splice_acceptor_variant_NMD_triggeringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002327

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
splice_acceptor_variantc
NMD_triggering_variantc

splice_donor_5th_base_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001787

has super-classes
splice_site_variantc

splice_donor_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002170

has super-classes
splice_region_variantc

splice_donor_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001575

has super-classes
splice_site_variantc
has sub-classes
splice_donor_variant_NMD_escapingc, splice_donor_variant_NMD_triggeringc

splice_donor_variant_NMD_escapingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002326

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
splice_donor_variantc
NMD_escaping_variantc

splice_donor_variant_NMD_triggeringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002325

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
splice_donor_variantc
NMD_triggering_variantc

splice_enhancerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000344

has super-classes
splicing_regulatory_regionc
has sub-classes
exonic_splice_enhancerc, intronic_splice_enhancerc

splice_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001421

has super-classes
junctionc

splice_polypyrimidine_tract_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002169

has super-classes
splicing_variantc

splice_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001902

has super-classes
primary_transcript_regionc
part_ofop some primary_transcriptc

splice_region_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001630

EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
has super-classes
splicing_variantc
has sub-classes
exonic_splice_region_variantc, non_coding_transcript_splice_region_variantc, splice_donor_region_variantc

splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000162

With spliceosomal introns, the splice sites bind the spliceosomal machinery.
has super-classes
primary_transcript_regionc
has sub-classes
cis_splice_sitec, cryptic_splice_sitec, trans_splice_sitec

splice_site_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001629

EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
has super-classes
splicing_variantc
intron_variantc
has sub-classes
splice_acceptor_variantc, splice_donor_5th_base_variantc, splice_donor_variantc

spliced_leader_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000636

has super-classes
primary_transcript_regionc
part_ofop some mini_exon_donor_RNAc

spliceosomal_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000662

GO:0000398.
has super-classes
intronc
has sub-classes
U12_intronc, U2_intronc

spliceosomal_intron_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000841

A terms added to allow the parts of introns to have is_a paths to the root.
has super-classes
primary_transcript_regionc
part_ofop some spliceosomal_intronc
has sub-classes
branch_sitec, polypyrimidine_tractc

splicing_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000682

splicing_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001056

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc
has sub-classes
splice_enhancerc

splicing_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001568

has super-classes
transcript_variantc
has sub-classes
cryptic_splice_site_variantc, exon_loss_variantc, extended_intronic_splice_region_variantc, intron_gain_variantc, splice_polypyrimidine_tract_variantc, splice_region_variantc, splice_site_variantc

spot_42_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000389

has super-classes
small_regulatory_ncRNAc

spurious_proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002248

Added as per request from GitHub Issue #478 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/478)
has super-classes
experimental_featurec

SRP_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000590

has super-classes
ncRNAc
derives_fromop some SRP_RNA_primary_transcriptc

SRP_RNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000642

has super-classes
non_protein_codingc

SRP_RNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001269

is equivalent to
ncRNA_genec and (has_qualityop some SRP_RNA_encodingc)
has super-classes
ncRNA_genec
has_qualityop some SRP_RNA_encodingc

SRP_RNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000589

has super-classes
nc_primary_transcriptc

ss_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000441

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
oligoc
has sub-classes
primerc

ss_RNA_viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001199

has super-classes
viral_sequencec
has sub-classes
ambisense_ssRNA_viral_sequencec, negative_sense_ssRNA_viral_sequencec, positive_sense_ssRNA_viral_sequencec

st_turn_left_handed_type_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001142

has super-classes
serine_threonine_turnc

st_turn_left_handed_type_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001143

has super-classes
serine_threonine_turnc

st_turn_right_handed_type_onec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001144

has super-classes
serine_threonine_turnc

st_turn_right_handed_type_twoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001145

has super-classes
serine_threonine_turnc

standard_draftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001486

has super-classes
whole_genome_sequence_statusc

start_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000318

has super-classes
codonc
has sub-classes
non_canonical_start_codonc

start_lostc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002012

Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
has super-classes
initiator_codon_variantc
nonsynonymous_variantc

start_retained_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002019

Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
has super-classes
initiator_codon_variantc
synonymous_variantc

statusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000905

This term is the hypernym of attributes and should not be annotated to.
has super-classes
feature_attributec
has sub-classes
consensusc, fragmentaryc, independently_knownc, invalidatedc, low_complexityc, predictedc, validatedc, whole_genome_sequence_statusc

status_of_coding_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001255

stemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002255

Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
has super-classes
stem_loop_regionc
has sub-classes
non_complimentary_stemc

stem_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000313

has super-classes
RNA_sequence_secondary_structurec
has sub-classes
tetraloopc

stem_loop_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002253

Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
has super-classes
RNA_sequence_secondary_structurec
part_ofop some stem_loopc
has sub-classes
loopc, stemc

sterol_regulatory_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001861

has super-classes
promoter_elementc

sticky_end_restriction_enzyme_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001692

has super-classes
restriction_enzyme_recognition_sitec
has sub-classes
five_prime_sticky_end_restriction_enzyme_cleavage_sitec, three_prime_sticky_end_restriction_enzyme_cleavage_sitec

stop_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000319

has super-classes
codonc
has sub-classes
amber_stop_codonc, ochre_stop_codonc, opal_stop_codonc

stop_codon_read_throughc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000883

has super-classes
recoded_codonc
has sub-classes
stop_codon_redefined_as_pyrrolysinec, stop_codon_redefined_as_selenocysteinec

stop_codon_readthroughc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001267

stop_codon_redefined_as_pyrrolysinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000884

has super-classes
stop_codon_read_throughc

stop_codon_redefined_as_selenocysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000885

has super-classes
stop_codon_read_throughc

stop_codon_redefinition_as_pyrrolysinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001270

stop_codon_redefinition_as_selenocysteinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001266

stop_codon_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001288

This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
has super-classes
recoding_stimulatory_regionc
has sub-classes
UAA_stop_codon_signalc, UAG_stop_codon_signalc, UGA_stop_codon_signalc

stop_gainedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001587

EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
has super-classes
feature_truncationc
nonsynonymous_variantc
has sub-classes
stop_gained_NMD_escapingc, stop_gained_NMD_triggeringc

stop_gained_NMD_escapingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002322

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
stop_gainedc
NMD_escaping_variantc

stop_gained_NMD_triggeringc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002321

Added as per request from Ang Roberts as part of GenCC November 2020.
has super-classes
stop_gainedc
NMD_triggering_variantc

stop_lostc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001578

EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
has super-classes
terminator_codon_variantc
feature_elongationc
nonsynonymous_variantc

stop_retained_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001567

has super-classes
terminator_codon_variantc
synonymous_variantc

strand_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000983

Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
has super-classes
feature_attributec
has sub-classes
doublec, singlec

STREP_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001859

has super-classes
promoter_elementc

stRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000656

has super-classes
non_protein_codingc

structural_alterationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001785

has super-classes
sequence_alterationc
has sub-classes
complex_structural_alterationc, rearrangement_regionc, translocationc

structural_interaction_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002093

Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they must be "interacting" and thus important for protein structure.
has super-classes
3D_polypeptide_structure_variantc

structural_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001537

has super-classes
sequence_variantc
has sub-classes
feature_ablationc, feature_amplificationc, feature_fusionc, feature_translocationc, feature_variantc, sequence_length_variantc

STSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000331

has super-classes
tagc

STS_mapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001251

has super-classes
fragment_assemblyc
has_partop some STSc

substitutec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000048

substitute_A_to_Ic back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000919

substitute_C_to_Uc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000922

substitutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000002

has super-classes
sequence_alterationc
biological_regionc
has sub-classes
MNVc, SNVc, complex_substitutionc

substitution_artifactc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002176

has super-classes
sequence_alteration_artifactc
has sub-classes
MNV_artifactc, SNV_artifactc

subtelomerec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001997

has super-classes
chromosomal_structural_elementc

sugar_edge_base_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000030

has super-classes
base_pairc

SUMO_interaction_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002235

Added as per request GitHub issue #434 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/434)
has super-classes
protein_protein_contactc

supercontigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000148

has super-classes
partial_genomic_sequence_assemblyc
part_ofop some ultracontigc
has sub-classes
mitochondrial_supercontigc, unassigned_supercontigc

supported_by_domain_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000908

has super-classes
supported_by_sequence_similarityc

supported_by_EST_or_cDNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000909

has super-classes
supported_by_sequence_similarityc

supported_by_sequence_similarityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000907

has super-classes
predictedc
has sub-classes
supported_by_EST_or_cDNAc, supported_by_domain_matchc

SVA_deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002068

has super-classes
mobile_element_deletionc

SVA_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002065

has super-classes
mobile_element_insertionc

symbiosis_islandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000776

Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
has super-classes
genomic_islandc

symmetric_RNA_internal_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000025

has super-classes
RNA_internal_loopc

synonymousc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001815

has super-classes
coding_variant_qualityc

synonymous_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001819

EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation). This term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
has super-classes
coding_sequence_variantc
has sub-classes
start_retained_variantc, stop_retained_variantc

syntenicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000860

has super-classes
conservedc

syntenic_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005858

is equivalent to
conserved_regionc and (has_qualityop some syntenicc)
has super-classes
conserved_regionc
has_qualityop some syntenicc

synthetic_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001247

has super-classes
oligoc
has sub-classes
GNA_oligoc, LNA_oligoc, PNA_oligoc, TNA_oligoc, morpholino_oligoc

synthetic_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000351

has super-classes
polymer_attributec
has sub-classes
designed_sequencec, random_sequencec

T3_RNA_Polymerase_Promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001206

has super-classes
Phage_RNA_Polymerase_Promoterc

T7_RNA_Polymerase_Promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001207

has super-classes
Phage_RNA_Polymerase_Promoterc

T_cell_receptor_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002133

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
vertebrate_immune_system_genec
has sub-classes
TR_C_Genec, TR_D_Genec, TR_J_Genec, TR_V_Genec

T_cell_receptor_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002099

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
vertebrate_immune_system_pseudogenec
has sub-classes
TR_J_pseudogenec, TR_V_pseudogenec

T_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001177

has super-classes
tRNA_regionc

T_to_A_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000021

has super-classes
pyrimidine_to_purine_transversionc

T_to_C_transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000013

has super-classes
pyrimidine_transitionc

T_to_G_transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000022

has super-classes
pyrimidine_to_purine_transversionc

tagc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000324

has super-classes
oligoc
has sub-classes
CAGE_tagc, ESTc, SAGE_tagc, STSc, engineered_tagc, multiplexing_sequence_identifierc

tandemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001513

has super-classes
insertion_attributec

tandem_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000173

has super-classes
duplicationc
has sub-classes
direct_tandem_duplicationc, inverted_tandem_duplicationc

tandem_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000705

has super-classes
repeat_regionc
has sub-classes
monomeric_repeatc, repeat_instability_regionc, satellite_DNAc

target_site_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000434

is equivalent to
direct_repeatc and (derives_fromop some transposable_elementc)
has super-classes
direct_repeatc
derives_fromop some transposable_elementc

targeting_vectorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001644

is equivalent to
vector_repliconc and (has_partop some homologous_regionc) and (has_qualityop some engineeredc)
has super-classes
vector_repliconc
engineered_regionc
has_qualityop some engineeredc
has_partop some homologous_regionc

tasiRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001800

has super-classes
ncRNAc
derives_fromop some tasiRNA_primary_transcriptc

tasiRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001801

has super-classes
nc_primary_transcriptc

TATA_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000174

Binds TBP.
has super-classes
core_eukaryotic_promoter_elementc
has sub-classes
RNA_polymerase_III_TATA_boxc, RNA_polymerase_II_TATA_boxc

Tc1_Mariner_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002278

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

TCS_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002044

Requested by Rama - SGD.
has super-classes
promoter_elementc

TCT_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001959

has super-classes
core_eukaryotic_promoter_elementc

teb1_recognition_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002258

Requested by Antonia Locke, (Pombe) as per GitHub Issue Request #439 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/439)
has super-classes
DNA_motifc

telomerase_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000390

has super-classes
ncRNAc

telomerase_RNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001643

has super-classes
ncRNA_genec

telomerec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000624

has super-classes
chromosomal_structural_elementc

telomeric_D_loopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002171

This definition is from GO:0061820 telomeric D-loop disassembly.
has super-classes
origin_of_replicationc

telomeric_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001496

The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
has super-classes
repeat_regionc
part_ofop some telomerec

telomeric_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001927

has super-classes
ncRNAc
has sub-classes
ARIAc, ARRETc, TERRAc, anti_ARRETc

template_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000978

has super-classes
guide_RNA_regionc

terminal_inverted_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000481

has super-classes
inverted_repeatc
part_ofop some terminal_inverted_repeat_elementc
has sub-classes
five_prime_terminal_inverted_repeatc, three_prime_terminal_inverted_repeatc

terminal_inverted_repeat_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000208

has super-classes
DNA_transposonc
has sub-classes
CACTA_TIR_transposonc, MITEc, Merlin_TIR_transposonc, Mutator_TIR_transposonc, PIF_Harbinger_TIR_transposonc, P_TIR_transposonc, Tc1_Mariner_TIR_transposonc, Transib_TIR_transposonc, hAT_TIR_transposonc, insertion_sequencec, piggyBac_TIR_transposonc, polintonc

terminal_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002201

has super-classes
repeat_regionc

terminatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000141

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc
part_ofop some transcriptc
has sub-classes
bacterial_terminatorc, eukaryotic_terminatorc

terminator_codon_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001590

The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
has super-classes
coding_sequence_variantc
has sub-classes
incomplete_terminal_codon_variantc, stop_lostc, stop_retained_variantc

terminator_of_type_2_RNApol_III_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000615

has super-classes
eukaryotic_terminatorc

TERRAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001923

Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
has super-classes
telomeric_transcriptc

tetraloopc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001008

has super-classes
stem_loopc

tetranucleotide_repeat_microsatellite_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000641

has super-classes
microsatellitec

TF_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000235

Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc
nucleotide_to_protein_binding_sitec
part_ofop some cis_regulatory_modulec
has sub-classes
GATA_boxc, ISREc, pheromone_response_elementc, retinoic_acid_responsive_elementc, transcription_factor_regulatory_sitec

TF_binding_site_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001782

has super-classes
regulatory_region_variantc

TFBS_ablationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001895

Created in conjunction with the EBI.
has super-classes
regulatory_region_ablationc

TFBS_amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001892

Created in conjunction with the EBI.
has super-classes
regulatory_region_amplificationc

TFBS_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001888

Created in conjunction with the EBI.
has super-classes
regulatory_region_fusionc

TFBS_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001885

Created in conjunction with the EBI.
has super-classes
regulatory_region_translocationc

TFRS_collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002297

Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc
has_partop some transcription_factor_regulatory_sitec

TFRS_modulec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002296

Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc
has_partop some transcription_factor_regulatory_sitec

theta_replicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000970

This has been obsoleted as it represents a process. replaced_by: GO:0070582

three_methylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001281

has super-classes
modified_cytidinec

three_methylpseudouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001377

has super-classes
modified_uridinec

three_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001372

has super-classes
modified_uridinec

three_prime_cis_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000164

has super-classes
cis_splice_sitec
has sub-classes
canonical_three_prime_splice_sitec, non_canonical_three_prime_splice_sitec

three_prime_clipc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000557

has super-classes
clipc

three_prime_coding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000202

has super-classes
coding_exonc

three_prime_coding_exon_coding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000197

has super-classes
coding_region_of_exonc
part_ofop some three_prime_coding_exonc

three_prime_coding_exon_noncoding_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000484

has super-classes
noncoding_region_of_exonc
part_ofop some three_prime_coding_exonc

three_prime_D_heptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000493

has super-classes
heptamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some three_prime_D_recombination_signal_sequencec

three_prime_D_nonamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000494

has super-classes
nonamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some three_prime_D_recombination_signal_sequencec

three_prime_D_recombination_signal_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000570

has super-classes
D_gene_recombination_featurec

three_prime_D_spacerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000495

has super-classes
vertebrate_immune_system_gene_recombination_spacerc
part_ofop some three_prime_D_recombination_signal_sequencec

three_prime_duplicated_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002246

Added as per request from the Illumina group
has super-classes
partially_duplicated_transcriptc

three_prime_ESTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001209

has super-classes
ESTc

three_prime_five_prime_overlapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000076

has super-classes
overlappingc

three_prime_flanking_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001417

has super-classes
flanking_regionc

three_prime_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000192

has super-classes
intronc

three_prime_LTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000426

has super-classes
long_terminal_repeatc

three_prime_LTR_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000849

has super-classes
LTR_componentc
part_ofop some three_prime_LTRc
has sub-classes
R_three_prime_LTR_regionc, U3_three_prime_LTR_regionc, U5_three_prime_LTR_regionc

three_prime_noncoding_exonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000444

has super-classes
noncoding_exonc

three_prime_overlapping_ncrnac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002120

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
has super-classes
ncRNAc

three_prime_RACE_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001433

has super-classes
cDNA_clonec

three_prime_recoding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001277

has super-classes
recoding_stimulatory_regionc
has sub-classes
distant_three_prime_recoding_signalc, flanking_three_prime_quadruplet_recoding_signalc, three_prime_repeat_recoding_signalc, three_prime_stem_loop_structurec

three_prime_repeat_recoding_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001286

has super-classes
three_prime_recoding_sitec

three_prime_restriction_enzyme_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001690

has super-classes
single_strand_restriction_enzyme_cleavage_sitec
part_ofop some sticky_end_restriction_enzyme_cleavage_sitec

three_prime_RSTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001468

has super-classes
RSTc

three_prime_stem_loop_structurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001279

has super-classes
three_prime_recoding_sitec

three_prime_sticky_end_restriction_enzyme_cleavage_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001976

Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
has super-classes
sticky_end_restriction_enzyme_cleavage_sitec

three_prime_terminal_inverted_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000421

has super-classes
terminal_inverted_repeatc

three_prime_three_prime_overlapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000075

has super-classes
overlappingc

three_prime_USTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001465

has super-classes
USTc

three_prime_UTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000205

has super-classes
UTRc

three_prime_UTR_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000448

has super-classes
UTR_intronc

three_ten_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001119

Range.
has super-classes
right_handed_peptide_helixc

three_three_amino_three_carboxypropyl_uridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001353

has super-classes
modified_uridinec

three_two_prime_O_dimethyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001375

has super-classes
modified_uridinec

threoninec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001445

A place holder for a cross product with chebi.
has super-classes
amino_acidc

threonine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000227

has super-classes
tRNA_primary_transcriptc

threonyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000270

has super-classes
tRNAc
derives_fromop some threonine_tRNA_primary_transcriptc

tiling_pathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000472

has super-classes
sequence_assemblyc

tiling_path_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000480

has super-classes
clonec
tiling_path_fragmentc

tiling_path_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000474

has super-classes
assembly_componentc
part_ofop some tiling_pathc
has sub-classes
tiling_path_clonec

tmRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000584

has super-classes
small_regulatory_ncRNAc

tmRNA_acceptor_piecec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000770

Added in response to Kelly Williams from Indiana. Date: Nov 2005.
has super-classes
tmRNA_regionc

tmRNA_coding_piecec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000769

Added in response to comment from Kelly Williams from Indiana. Nov 2005.
has super-classes
tmRNA_regionc

tmRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000659

has super-classes
non_protein_codingc

tmRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001271

Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
is equivalent to
sncRNA_genec and (has_qualityop some tmRNA_encodingc)
has super-classes
sncRNA_genec
has_qualityop some tmRNA_encodingc

tmRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000586

has super-classes
nc_primary_transcriptc

tmRNA_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000847

This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
has super-classes
mature_transcript_regionc
part_ofop some tmRNAc
has sub-classes
tmRNA_acceptor_piecec, tmRNA_coding_piecec

TNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001190

Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
has super-classes
nucleic_acidc

TNA_oligoc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001191

is equivalent to
synthetic_oligoc and (has_qualityop some TNAc)
has super-classes
synthetic_oligoc
has_qualityop some TNAc

tnaORFc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002029

has super-classes
ORFc

topologically_associated_domainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002304

Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
has super-classes
topologically_defined_regionc

topologically_associated_domain_boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002305

Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
has super-classes
junctionc
part_ofop some topologically_associated_domainc

topologically_defined_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001412

has super-classes
regionc
has sub-classes
flanking_regionc, repeat_componentc, topologically_associated_domainc

topology_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000986

Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
has super-classes
polymer_attributec
has sub-classes
circularc, linearc

TR_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001858

has super-classes
promoter_elementc

TR_C_Genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002134

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
T_cell_receptor_genec

TR_D_Genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002135

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
T_cell_receptor_genec

TR_J_Genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002136

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
T_cell_receptor_genec

TR_J_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002104

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
T_cell_receptor_pseudogenec

TR_V_Genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002137

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
T_cell_receptor_genec

TR_V_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002103

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
T_cell_receptor_pseudogenec

trans_splice_acceptor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000706

This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
has super-classes
trans_splice_sitec
has sub-classes
SL1_acceptor_sitec, SL2_acceptor_sitec

trans_splice_donor_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000707

SL RNA contains a donor site.
has super-classes
trans_splice_sitec

trans_splice_junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001474

has super-classes
junctionc

trans_splice_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001420

has super-classes
splice_sitec
has sub-classes
trans_splice_acceptor_sitec, trans_splice_donor_sitec

trans_splicedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000870

has super-classes
transcript_attributec

trans_spliced_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000872

is equivalent to
mRNAc and (adjacent_toop some spliced_leader_RNAc) and (has_qualityop some trans_splicedc)
has super-classes
mRNAc
trans_spliced_transcriptc
adjacent_toop some spliced_leader_RNAc
has_qualityop some trans_splicedc

trans_spliced_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000479

is equivalent to
transcriptc and (has_qualityop some trans_splicedc)
has super-classes
transcriptc
has_qualityop some trans_splicedc
has sub-classes
trans_spliced_mRNAc

transcribed_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001457

This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
has super-classes
experimental_featurec
has_partop some reagentc
has sub-classes
unigene_clusterc

transcribed_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001418

Term requested by the MODencode group.
has super-classes
experimental_featurec

transcribed_processed_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002109

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
processed_pseudogenec

transcribed_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000502

This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.

transcribed_spacer_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000638

has super-classes
rRNA_primary_transcript_regionc
has sub-classes
external_transcribed_spacer_regionc, internal_transcribed_spacer_regionc

transcribed_unitary_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002108

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
unitary_pseudogenec

transcribed_unprocessed_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002107

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
non_processed_pseudogenec

transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000673

Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.
has super-classes
gene_member_regionc
overlapsop some unit_of_gene_expressionc
has sub-classes
aberrant_processed_transcriptc, alternatively_spliced_transcriptc, edited_transcriptc, enzymatic_RNAc, long_terminal_repeat_transcriptc, mature_transcriptc, monocistronic_transcriptc, polycistronic_transcriptc, predicted_transcriptc, primary_transcriptc, processed_transcriptc, trans_spliced_transcriptc, transcript_bound_by_nucleic_acidc, transcript_bound_by_proteinc, transcript_with_translational_frameshiftc

transcript_ablationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001893

Created in conjunction with the EBI.
has super-classes
feature_ablationc

transcript_amplificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001889

Created in conjunction with the EBI.
has super-classes
feature_amplificationc

transcript_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000237

has super-classes
feature_attributec
has sub-classes
alternatively_splicedc, cappedc, editedc, mRNA_attributec, monocistronicc, polycistronicc, trans_splicedc

transcript_bound_by_nucleic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000278

Formerly called transcript_by_bound_nucleic_acid.
is equivalent to
transcriptc and (has_qualityop some bound_by_nucleic_acidc)
has super-classes
transcriptc
has_qualityop some bound_by_nucleic_acidc

transcript_bound_by_proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000279

Formerly called transcript_by_bound_protein.
is equivalent to
transcriptc and (has_qualityop some bound_by_proteinc)
has super-classes
transcriptc
has_qualityop some bound_by_proteinc

transcript_edited_by_U_insertion/deletionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000597

transcript_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000115

transcript_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001538

has super-classes
functionally_abnormalc
has sub-classes
level_of_transcript_variantc, transcript_processing_variantc, transcript_stability_variantc, transcription_variantc

transcript_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001886

Created in conjunction with the EBI.
has super-classes
feature_fusionc

transcript_processing_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001543

has super-classes
transcript_function_variantc
has sub-classes
editing_variantc, polyadenylation_variantc

transcript_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000833

This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
has super-classes
biological_regionc
part_ofop some transcriptc
has sub-classes
anchor_binding_sitec, edited_transcript_featurec, exonc, exon_regionc, mature_transcript_regionc, primary_transcript_regionc, ribonuclease_sitec

transcript_regulatory_region_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001890

Created in conjunction with the EBI.
has super-classes
feature_fusionc

transcript_secondary_structure_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001596

has super-classes
transcript_variantc
has sub-classes
compensatory_transcript_secondary_structure_variantc

transcript_sequence_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001579

transcript_stability_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001546

has super-classes
transcript_function_variantc
has sub-classes
decreased_transcript_stability_variantc, increased_transcript_stability_variantc

transcript_translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001883

Created in conjunction with the EBI.
has super-classes
feature_translocationc

transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001576

has super-classes
gene_variantc
has sub-classes
NMD_transcript_variantc, coding_transcript_variantc, complex_transcript_variantc, exon_variantc, incomplete_transcript_variantc, intragenic_variantc, intron_variantc, non_coding_transcript_variantc, partially_duplicated_transcriptc, splicing_variantc, transcript_secondary_structure_variantc

transcript_with_readthrough_stop_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000117

transcript_with_translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000118

is equivalent to
transcriptc and (has_qualityop some translationally_frameshiftedc)
has super-classes
transcriptc
has_qualityop some translationally_frameshiftedc

transcription_end_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000616

has super-classes
primary_transcript_regionc

transcription_factor_regulatory_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002295

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
TF_binding_sitec

transcription_pause_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002047

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
transcriptional_cis_regulatory_regionc

transcription_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001679

Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527.

transcription_start_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001915

has super-classes
experimental_featurec
has sub-classes
CAGE_clusterc

transcription_termination_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002213

has super-classes
eukaryotic_terminatorc

transcription_unitc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002301

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
unit_of_gene_expressionc

transcription_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001549

has super-classes
transcript_function_variantc
has sub-classes
rate_of_transcription_variantc

transcriptional_cis_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001055

Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527.
has super-classes
regulatory_regionc
has sub-classes
TFRS_collectionc, TFRS_modulec, TF_binding_sitec, cis_regulatory_frameshift_elementc, cis_regulatory_modulec, intronic_regulatory_regionc, operatorc, polyA_signal_sequencec, promoterc, promoter_flanking_regionc, promoter_targeting_sequencec, response_elementc, splicing_regulatory_regionc, terminatorc, transcription_pause_sitec

transcriptionally_constitutivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000124

has super-classes
transcriptionally_regulatedc

transcriptionally_inducedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000125

has super-classes
transcriptionally_regulatedc
has sub-classes
positively_autoregulatedc

transcriptionally_regulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000123

By:<protein_id>.
has super-classes
regulatedc
has sub-classes
autoregulatedc, transcriptionally_constitutivec, transcriptionally_inducedc, transcriptionally_repressedc

transcriptionally_repressedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000126

has super-classes
transcriptionally_regulatedc
has sub-classes
negatively_autoregulatedc, silencedc

transgenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000902

is equivalent to
genec and (has_qualityop some transgenicc)
has super-classes
genec
has_qualityop some transgenicc
has sub-classes
floxed_genec

transgene_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000452

transgenicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000781

has super-classes
feature_attributec

transgenic_insertionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001218

is equivalent to
insertionc and (has_qualityop some transgenicc)
has super-classes
insertionc
has_qualityop some transgenicc

transgenic_transposable_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000796

Modified as requested by Lynn - FB. May 2007.
is equivalent to
transposable_elementc and (derives_fromop some clonec) and (has_qualityop some transgenicc)
has super-classes
transposable_elementc
has_qualityop some transgenicc
derives_fromop some clonec

Transib_TIR_transposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002282

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
terminal_inverted_repeat_elementc

transit_peptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000725

Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
has super-classes
peptide_localization_signalc
derives_fromop some transit_peptide_region_of_CDSc

transit_peptide_region_of_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002252

Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
has super-classes
CDS_regionc

transitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000009

has super-classes
SNVc
has sub-classes
purine_transitionc, pyrimidine_transitionc

translated_nucleotide_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000181

has super-classes
nucleotide_matchc

translated_processed_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002105

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
processed_pseudogenec

translated_unprocessed_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002106

Term added as part of collaboration with Gencode, adding biotypes used in annotation.
has super-classes
non_processed_pseudogenec

translation_regulatory_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001680

has super-classes
regulatory_regionc
has sub-classes
attenuatorc

translational_frameshiftc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001210

Added synonym 'ribosomal_slippage' on Feb 1, 2021, a term in INSDC and GenBank. See GitHub Issue #522.
has super-classes
mRNA_regionc
has sub-classes
minus_1_translational_frameshiftc, minus_2_translational_frameshiftc, plus_1_translational_frameshiftc, plus_2_translational_frameshiftc

translational_product_function_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001539

has super-classes
functionally_abnormalc
has sub-classes
3D_polypeptide_structure_variantc, complex_change_of_translational_product_variantc, polypeptide_function_variantc, translational_product_level_variantc

translational_product_level_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001553

has super-classes
translational_product_function_variantc
has sub-classes
decreased_translational_product_levelc, increased_translational_product_levelc

translational_product_structure_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001598

has super-classes
gene_variantc
has sub-classes
polypeptide_sequence_variantc

translationally_frameshiftedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000887

has super-classes
recodedc
has sub-classes
minus_1_translationally_frameshiftedc, plus_1_translationally_frameshiftedc

translationally_regulatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000131

has super-classes
regulatedc

translationally_regulated_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000896

is equivalent to
genec and (has_qualityop some translationally_regulatedc)
has super-classes
genec
has_qualityop some translationally_regulatedc

translocatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000049

translocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000199

has super-classes
structural_alterationc
has sub-classes
chromosomal_translocationc

translocation_breakpointc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001413

has super-classes
chromosome_breakpointc

translocation_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000686

has super-classes
chromosomal_translocationc

translocaton_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001520

has super-classes
alteration_attributec
has sub-classes
insertionalc, reciprocalc

transmembrane_helixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001812

has super-classes
peptide_helixc
part_ofop some transmembrane_polypeptide_regionc

transmembrane_polypeptide_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001077

has super-classes
intramembrane_polypeptide_regionc

transposable_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000101

has super-classes
integrated_mobile_genetic_elementc
has sub-classes
DNA_transposonc, engineered_transposable_elementc, foreign_transposable_elementc, natural_transposable_elementc, nested_transposonc, retrotransposonc, transgenic_transposable_elementc

transposable_element_attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000780

Added by KE Jan 2006 to capture the kinds of attributes of TEs

transposable_element_CDSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001896

is equivalent to
CDSc and (part_ofop some transposable_elementc)
has super-classes
CDSc
part_ofop some transposable_elementc

transposable_element_flanking_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000364

has super-classes
flanking_regionc

transposable_element_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000111

is equivalent to
genec and (part_ofop some transposable_elementc)
has super-classes
genec
part_ofop some transposable_elementc
has sub-classes
engineered_foreign_transposable_element_genec

transposable_element_insertion_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000368

has super-classes
insertion_sitec

transposable_element_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001897

is equivalent to
pseudogenec and (part_ofop some transposable_elementc)
has super-classes
pseudogenec
part_ofop some transposable_elementc

transposon_fragmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001054

has super-classes
repeat_componentc
part_ofop some nested_transposonc

transversionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000017

has super-classes
SNVc
has sub-classes
purine_to_pyrimidine_transversionc, pyrimidine_to_purine_transversionc

TRIMc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002261

Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429)
has super-classes
LTR_retrotransposonc

trinucleotide_repeat_expansionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002165

has super-classes
short_tandem_repeat_expansionc

trinucleotide_repeat_microsatellite_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000291

has super-classes
microsatellitec
has sub-classes
GTT_trinucleotide_repeatc

tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000253

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
sncRNAc
derives_fromop some tRNA_primary_transcriptc
has sub-classes
alanyl_tRNAc, arginyl_tRNAc, asparaginyl_tRNAc, aspartyl_tRNAc, cysteinyl_tRNAc, glutaminyl_tRNAc, glutamyl_tRNAc, glycyl_tRNAc, histidyl_tRNAc, isoleucyl_tRNAc, leucyl_tRNAc, lysyl_tRNAc, methionyl_tRNAc, mt_tRNAc, phenylalanyl_tRNAc, prolyl_tRNAc, pyrrolysyl_tRNAc, selenocysteinyl_tRNAc, seryl_tRNAc, threonyl_tRNAc, tryptophanyl_tRNAc, tyrosyl_tRNAc, valyl_tRNAc

tRNA_encodingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000663

has super-classes
non_protein_codingc

tRNA_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001272

Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
is equivalent to
sncRNA_genec and (has_qualityop some tRNA_encodingc)
has super-classes
sncRNA_genec
has_qualityop some tRNA_encodingc

tRNA_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001272

Could be a cross product with Gene ontology, GO:0006388.
has super-classes
endonuclease_spliced_intronc

tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000210

has super-classes
nc_primary_transcriptc
has sub-classes
alanine_tRNA_primary_transcriptc, arginine_tRNA_primary_transcriptc, asparagine_tRNA_primary_transcriptc, aspartic_acid_tRNA_primary_transcriptc, cysteine_tRNA_primary_transcriptc, glutamic_acid_tRNA_primary_transcriptc, glutamine_tRNA_primary_transcriptc, glycine_tRNA_primary_transcriptc, histidine_tRNA_primary_transcriptc, isoleucine_tRNA_primary_transcriptc, leucine_tRNA_primary_transcriptc, lysine_tRNA_primary_transcriptc, methionine_tRNA_primary_transcriptc, miR_encoding_tRNA_primary_transcriptc, phenylalanine_tRNA_primary_transcriptc, proline_tRNA_primary_transcriptc, pyrrolysine_tRNA_primary_transcriptc, selenocysteine_tRNA_primary_transcriptc, serine_tRNA_primary_transcriptc, threonine_tRNA_primary_transcriptc, tryptophan_tRNA_primary_transcriptc, tyrosine_tRNA_primary_transcriptc, valine_tRNA_primary_transcriptc

tRNA_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001172

has super-classes
mature_transcript_regionc
part_ofop some tRNAc
has sub-classes
CCA_tailc, DHU_loopc, T_loopc, anticodonc, anticodon_loopc

tRNA_SINE_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002274

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
SINE_elementc

tryptophanc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001440

A place holder for a cross product with chebi.
has super-classes
amino_acidc

tryptophan_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000228

has super-classes
tRNA_primary_transcriptc

tryptophanyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000271

has super-classes
tRNAc
derives_fromop some tryptophan_tRNA_primary_transcriptc

TSSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000315

Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant.
has super-classes
primary_transcript_regionc
core_promoter_elementc
has sub-classes
major_TSSc, minor_TSSc

TSS_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001240

Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528

twintronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000406

has super-classes
intronc

two_methyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001296

has super-classes
modified_adenosinec

two_methylthio_N6_cis_hydroxyisopentenyl_adenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001303

has super-classes
modified_adenosinec

two_methylthio_N6_hydroxynorvalyl_carbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001309

has super-classes
modified_adenosinec

two_methylthio_N6_isopentenyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001301

has super-classes
modified_adenosinec

two_methylthio_N6_methyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001299

has super-classes
modified_adenosinec

two_methylthio_N6_threonyl_carbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001306

has super-classes
modified_adenosinec

two_prime_O_methyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001298

has super-classes
modified_adenosinec

two_prime_O_methylcytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001283

has super-classes
modified_cytidinec

two_prime_O_methylguanosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001327

has super-classes
modified_guanosinec

two_prime_O_methylinosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001280

has super-classes
modified_inosinec

two_prime_O_methylpseudouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001348

has super-classes
modified_uridinec

two_prime_O_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001345

has super-classes
modified_uridinec

two_prime_O_ribosyladenosine_phosphatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001310

has super-classes
modified_adenosinec

two_prime_O_ribosylguanosine_phosphatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001331

has super-classes
modified_guanosinec

two_thio_two_prime_O_methyluridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001352

has super-classes
modified_uridinec

two_thiocytidinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001284

has super-classes
modified_cytidinec

two_thiouridinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001349

has super-classes
modified_uridinec

type_I_enzyme_restriction_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000284

type_II_enzyme_restriction_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000304

tyrosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001446

A place holder for a cross product with chebi.
has super-classes
amino_acidc

tyrosine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000229

has super-classes
tRNA_primary_transcriptc

tyrosyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000272

has super-classes
tRNAc
derives_fromop some tyrosine_tRNA_primary_transcriptc

U11_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000398

has super-classes
snRNAc

U12_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000295

May have either GT-AC or AT-AC 5' and 3' boundaries.
has super-classes
spliceosomal_intronc

U12_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000399

has super-classes
snRNAc

U14_snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000403

An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
has super-classes
C_D_box_snoRNAc
derives_fromop some U14_snoRNA_primary_transcriptc

U14_snoRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005837

has super-classes
snoRNA_primary_transcriptc

U1_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000391

has super-classes
snRNAc

U2_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000184

May have either GT-AG or AT-AG 5' and 3' boundaries.
has super-classes
spliceosomal_intronc

U2_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000392

has super-classes
snRNAc

U3_five_prime_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000429

has super-classes
U3_LTR_regionc
five_prime_LTR_componentc

U3_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000424

has super-classes
LTR_componentc
has sub-classes
U3_five_prime_LTR_regionc

U3_snoRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001179

The definition is most of the old definition for snoRNA (SO:0000275).
has super-classes
C_D_box_snoRNAc

U3_three_prime_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000431

has super-classes
three_prime_LTR_componentc

U4_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000393

has super-classes
snRNAc

U4atac_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000394

has super-classes
snRNAc

U5_five_prime_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000428

has super-classes
U5_LTR_regionc
five_prime_LTR_componentc

U5_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000422

has super-classes
LTR_componentc
has sub-classes
U5_five_prime_LTR_regionc

U5_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000395

has super-classes
snRNAc

U5_three_prime_LTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000432

has super-classes
three_prime_LTR_componentc

U6_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000396

has super-classes
snRNAc

U6atac_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000397

has super-classes
snRNAc

U7_snRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002338

Added as a request from FlyBase. See GitHub Issue #508
has super-classes
snRNAc

U_boxc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001788

has super-classes
conserved_regionc
part_ofop some LTR_retrotransposonc

UAA_stop_codon_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001283

has super-classes
stop_codon_signalc

UAG_stop_codon_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001282

has super-classes
stop_codon_signalc

UGA_stop_codon_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1001285

has super-classes
stop_codon_signalc

ultracontigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000719

has super-classes
partial_genomic_sequence_assemblyc

UNAAAC_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002207

has super-classes
RNA_stability_elementc

unassigned_supercontigc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001875

Requested by Bayer Cropscience January, 2012.
has super-classes
supercontigc

uncharacterized_chromosomal_mutationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000170

has super-classes
chromosome_structure_variationc
has sub-classes
partially_characterized_chromosomal_mutationc

unconfirmed_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002139

has super-classes
predicted_transcriptc

undermodified_hydroxywybutosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001335

has super-classes
modified_guanosinec

unedited_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000607

has super-classes
edited_transcript_featurec

unequally_crossed_overc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000901

unidirectional_gene_fusionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002085

Requested by SNPEFF team. Feb 2016.
has super-classes
gene_fusionc

unigene_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001458

This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
has super-classes
transcribed_clusterc

uninverted_insertional_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000152

has super-classes
insertional_duplicationc

uninverted_interchromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000157

has super-classes
interchromosomal_transpositionc

uninverted_intrachromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000159

is equivalent to
intrachromosomal_transpositionc and (has_partop some directc)
has super-classes
intrachromosomal_transpositionc
has_partop some directc

unique_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001764

has super-classes
variant_frequencyc

unit_of_gene_expressionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002300

Added as per Mejia-Almonte et.al PMID:32665585
has super-classes
biological_regionc
has sub-classes
transcription_unitc

unitary_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001759

This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
has super-classes
non_processed_pseudogenec
has sub-classes
allelic_pseudogenec, transcribed_unitary_pseudogenec

unitary_pseudogenic_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002195

has super-classes
pseudogenic_rRNAc

unitary_pseudogenic_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002199

has super-classes
pseudogenic_tRNAc

unoriented_insertional_duplicationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000160

Flag - unknown in the definition.
has super-classes
insertional_duplicationc

unoriented_interchromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000161

FLAG - term describes an unknown.
has super-classes
interchromosomal_transpositionc

unoriented_intrachromosomal_transpositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000162

FLAG - definition describes an unknown.
has super-classes
intrachromosomal_transpositionc

unprocessed_pseudogenic_rRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002194

has super-classes
pseudogenic_rRNAc

unprocessed_pseudogenic_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002198

has super-classes
pseudogenic_tRNAc

unspecified_indelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002217

This term is used when there is a change that is either an insertion or a deletion but it is unknown which event occurred.
has super-classes
sequence_alterationc

untranslated_region_polycistronic_mRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000242

has super-classes
UTRc

uORFc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002027

has super-classes
ORFc
has sub-classes
AUG_initiated_uORFc, non_AUG_initiated_uORFc

UPDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001744

has super-classes
sequence_alterationc
has sub-classes
maternal_uniparental_disomyc, paternal_uniparental_disomyc

upstream_AUG_codonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000630

has super-classes
UTR_regionc
part_ofop some UTRc

upstream_gene_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001631

Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
has super-classes
intergenic_variantc
has sub-classes
2KB_upstream_variantc, 5KB_upstream_variantc

upstream_transcript_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001986

Requested by Graham Ritchie, EBI/Sanger.
has super-classes
intergenic_variantc

uridine_five_oxyacetic_acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001356

has super-classes
modified_uridinec

uridine_five_oxyacetic_acid_methyl_esterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001357

has super-classes
modified_uridinec

USTc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001464

has super-classes
ESTc
has sub-classes
five_prime_USTc, three_prime_USTc

UST_matchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001470

has super-classes
expressed_sequence_matchc

UTRc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000203

has super-classes
mRNA_regionc
has sub-classes
five_prime_UTRc, internal_UTRc, three_prime_UTRc, untranslated_region_polycistronic_mRNAc

UTR_intronc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000446

has super-classes
intronc
has sub-classes
five_prime_UTR_intronc, three_prime_UTR_intronc

UTR_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000837

A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
has super-classes
mRNA_regionc
has sub-classes
AU_rich_elementc, Bruno_response_elementc, iron_responsive_elementc, pumilio_response_elementc, upstream_AUG_codonc

UTR_variantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001622

has super-classes
exon_variantc
coding_transcript_variantc
has sub-classes
3_prime_UTR_variantc, 5_prime_UTR_variantc

V_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000526

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some V_gene_segmentc

V_D_DJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000527

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some V_gene_segmentc
has_partop some DJ_gene_segmentc
has_partop some C_gene_segmentc
has_partop some D_gene_segmentc

V_D_DJ_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000528

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some D_gene_segmentc
has_partop some V_gene_segmentc
has_partop some DJ_gene_segmentc

V_D_DJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000529

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some D_gene_segmentc
has_partop some J_gene_segmentc
has_partop some DJ_gene_segmentc
has_partop some C_gene_segmentc
has_partop some V_gene_segmentc

V_D_DJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000530

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some J_gene_segmentc
has_partop some DJ_gene_segmentc
has_partop some V_gene_segmentc
has_partop some D_gene_segmentc

V_D_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000531

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some C_gene_segmentc
has_partop some D_gene_segmentc
has_partop some J_gene_segmentc
has_partop some V_gene_segmentc

V_D_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000532

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some D_gene_segmentc
has_partop some J_gene_segmentc
has_partop some V_gene_segmentc

V_DJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000542

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some V_gene_segmentc
has_partop some C_gene_segmentc
has_partop some DJ_gene_segmentc

V_DJ_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000518

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some DJ_gene_segmentc
has_partop some V_gene_segmentc

V_DJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000564

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some DJ_gene_segmentc
has_partop some C_gene_segmentc
has_partop some V_gene_segmentc
has_partop some J_gene_segmentc

V_DJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000519

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some J_gene_segmentc
has_partop some DJ_gene_segmentc
has_partop some V_gene_segmentc

V_gene_recombination_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000538

has super-classes
vertebrate_immune_system_gene_recombination_signal_featurec

V_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000466

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_segmentc

V_heptamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000533

has super-classes
heptamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some V_gene_recombination_featurec

V_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000535

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some J_gene_segmentc
has_partop some C_gene_segmentc
has_partop some V_gene_segmentc

V_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000534

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc
has_partop some V_gene_segmentc
has_partop some J_gene_segmentc

V_nonamerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000536

has super-classes
nonamer_of_recombination_feature_of_vertebrate_immune_system_genec
part_ofop some V_gene_recombination_featurec

V_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001833

has super-classes
immunoglobulin_regionc

V_spacerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000537

has super-classes
vertebrate_immune_system_gene_recombination_spacerc
part_ofop some V_gene_recombination_featurec

V_VDJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000520

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some VDJ_gene_segmentc
has_partop some V_gene_segmentc
has_partop some C_gene_segmentc

V_VDJ_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000521

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some V_gene_segmentc
has_partop some VDJ_gene_segmentc

V_VDJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000565

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some VDJ_gene_segmentc
has_partop some V_gene_segmentc
has_partop some J_gene_segmentc
has_partop some C_gene_segmentc

V_VDJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000522

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some J_gene_segmentc
has_partop some VDJ_gene_segmentc
has_partop some V_gene_segmentc

V_VJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000523

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some V_gene_segmentc
has_partop some C_gene_segmentc
has_partop some VJ_gene_segmentc

V_VJ_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000524

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some V_gene_segmentc
has_partop some VJ_gene_segmentc

V_VJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000566

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some C_gene_segmentc
has_partop some J_gene_segmentc
has_partop some VJ_gene_segmentc
has_partop some V_gene_segmentc

V_VJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000525

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some VJ_gene_segmentc
has_partop some V_gene_segmentc
has_partop some J_gene_segmentc

vacuolar_sorting_signalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001813

has super-classes
peptide_localization_signalc

validatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000789

has super-classes
statusc
has sub-classes
experimentally_determinedc

validated_cDNA_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000808

is equivalent to
cDNA_clonec and (has_qualityop some validatedc)
has super-classes
cDNA_clonec
has_qualityop some validatedc

valinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001436

A place holder for a cross product with chebi.
has super-classes
amino_acidc

valine_tRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000230

has super-classes
tRNA_primary_transcriptc

valyl_tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000273

has super-classes
tRNAc
derives_fromop some valine_tRNA_primary_transcriptc

variant_collectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001507

is equivalent to
sequence_collectionc and (has_partop some sequence_alterationc)
has super-classes
sequence_collectionc
has_partop some sequence_alterationc
has sub-classes
allelec, chromosome_variationc, diplotypec, genotypec, haplotypec

variant_frequencyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001763

has super-classes
variant_qualityc
has sub-classes
allelic_frequencyc, common_variantc, fixed_variantc, polymorphic_variantc, rare_variantc, unique_variantc

variant_genomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001506

has super-classes
genomec
has sub-classes
chromosomally_aberrant_genomec

variant_originc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001762

has super-classes
variant_qualityc
has sub-classes
de_novo_variantc, germline_variantc, maternal_variantc, paternal_variantc, pedigree_specific_variantc, population_specific_variantc, somatic_variantc

variant_phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001769

has super-classes
variant_qualityc
has sub-classes
benign_variantc, disease_associated_variantc, disease_causing_variantc, quantitative_variantc

variant_qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001761

has super-classes
sequence_attributec
has sub-classes
coding_variant_qualityc, variant_frequencyc, variant_originc, variant_phenotypec

vault_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000404

has super-classes
ncRNAc

vaultRNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002040

has super-classes
nc_primary_transcriptc
has sub-classes
miR_encoding_vaultRNA_primary_transcriptc

VD_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000510

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segmentc

VDJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000541

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some VDJ_gene_segmentc
has_partop some C_gene_segmentc

VDJ_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000574

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segmentc

VDJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000487

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some C_gene_segmentc
has_partop some J_gene_segmentc
has_partop some VDJ_gene_segmentc

VDJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000488

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some VDJ_gene_segmentc
has_partop some J_gene_segmentc

vector_repliconc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000440

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
repliconc
part_ofop some clonec
has sub-classes
BACc, PACc, YACc, cosmidc, fosmidc, lambda_vectorc, phagemidc, plasmid_vectorc, targeting_vectorc

vertebrate_immune_system_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000937

vertebrate_immune_system_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002121

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
genec
has sub-classes
T_cell_receptor_genec, immunoglobulin_genec

vertebrate_immune_system_gene_recombination_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000301

has super-classes
recombination_feature_of_rearranged_genec
has sub-classes
N_regionc, S_regionc, vertebrate_immune_system_gene_recombination_signal_featurec, vertebrate_immune_system_gene_recombination_spacerc, vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc, vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc, vertebrate_immunoglobulin_T_cell_receptor_rearranged_segmentc, vertebrate_immunoglobulin_T_cell_receptor_segmentc

vertebrate_immune_system_gene_recombination_signal_featurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000939

has super-classes
vertebrate_immune_system_gene_recombination_featurec
has sub-classes
D_gene_recombination_featurec, J_gene_recombination_featurec, V_gene_recombination_featurec, heptamer_of_recombination_feature_of_vertebrate_immune_system_genec, nonamer_of_recombination_feature_of_vertebrate_immune_system_genec

vertebrate_immune_system_gene_recombination_spacerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000563

has super-classes
vertebrate_immune_system_gene_recombination_featurec
has sub-classes
J_spacerc, V_spacerc, five_prime_D_spacerc, three_prime_D_spacerc

vertebrate_immune_system_pseudogenec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002097

These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
has super-classes
pseudogenec
has sub-classes
T_cell_receptor_pseudogenec, immunoglobulin_pseudogenec

vertebrate_immunoglobulin_T_cell_receptor_gene_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000482

has super-classes
vertebrate_immune_system_gene_recombination_featurec
has sub-classes
C_clusterc, D_J_C_clusterc, D_J_clusterc, D_clusterc, J_C_clusterc, J_clusterc, V_J_C_clusterc, V_J_clusterc, V_clusterc

vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000938

has super-classes
vertebrate_immune_system_gene_recombination_featurec
has sub-classes
DJ_C_clusterc, DJ_J_C_clusterc, DJ_J_clusterc, D_DJ_C_clusterc, D_DJ_J_C_clusterc, D_DJ_J_clusterc, D_DJ_clusterc, VDJ_C_clusterc, VDJ_J_C_clusterc, VDJ_J_clusterc, VJ_C_clusterc, VJ_J_C_clusterc, VJ_J_clusterc, V_DJ_C_clusterc, V_DJ_J_C_clusterc, V_DJ_J_clusterc, V_DJ_clusterc, V_D_DJ_C_clusterc, V_D_DJ_J_C_clusterc, V_D_DJ_J_clusterc, V_D_DJ_clusterc, V_D_J_C_clusterc, V_D_J_clusterc, V_VDJ_C_clusterc, V_VDJ_J_C_clusterc, V_VDJ_J_clusterc, V_VDJ_clusterc, V_VJ_C_clusterc, V_VJ_J_C_clusterc, V_VJ_J_clusterc, V_VJ_clusterc

vertebrate_immunoglobulin_T_cell_receptor_rearranged_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000936

has super-classes
vertebrate_immune_system_gene_recombination_featurec
has sub-classes
DJ_gene_segmentc, VDJ_gene_segmentc, VD_gene_segmentc, VJ_gene_segmentc

vertebrate_immunoglobulin_T_cell_receptor_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000460

I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
has super-classes
vertebrate_immune_system_gene_recombination_featurec
has sub-classes
C_gene_segmentc, D_gene_segmentc, J_gene_segmentc, V_gene_segmentc

Viper_YR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002289

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
YR_retrotransposonc

viral_promoterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002311

has super-classes
promoterc
has sub-classes
Phage_RNA_Polymerase_Promoterc

viral_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001041

The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
has super-classes
extrachromosomal_mobile_genetic_elementc
repliconc
has sub-classes
ds_DNA_viral_sequencec, ds_RNA_viral_sequencec, phage_sequencec, ss_RNA_viral_sequencec

virtual_sequencec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000499

has super-classes
sequence_assemblyc

VJ_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000489

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some C_gene_segmentc
has_partop some VJ_gene_segmentc

VJ_gene_segmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000576

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segmentc

VJ_J_C_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000490

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some C_gene_segmentc
has_partop some J_gene_segmentc
has_partop some VJ_gene_segmentc

VJ_J_clusterc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000491

has super-classes
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterc
has_partop some J_gene_segmentc
has_partop some VJ_gene_segmentc

W_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002024

MERGED COMMENT: TARGET COMMENT: Requested by Janos Demeter, SGD. -------------------- SOURCE COMMENT: Requested by Janos Demeter, SGD.
has super-classes
mating_type_region_motifc

Watson_strandc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002262

Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419)
has super-classes
chromosome_partc

WC_base_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000029

has super-classes
base_pairc

whole_genome_sequence_statusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001499

This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
has super-classes
statusc
has sub-classes
annotation_directed_improved_draftc, finished_genomec, high_quality_draftc, improved_high_quality_draftc, noncontiguous_finishedc, standard_draftc

wild_typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000817

has super-classes
feature_attributec

wild_type_rescue_genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000818

is equivalent to
genec and (has_qualityop some wild_typec)
has super-classes
rescue_genec
has_qualityop some wild_typec

wobble_base_pairc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001015

has super-classes
base_pairc

wybutosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001332

has super-classes
modified_guanosinec

wyosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001336

has super-classes
modified_guanosinec

X_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001497

Possible functions include roles in chromosomal segregation, maintenance of chromosome stability, recombinational sequestering, or as a barrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. From Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.
has super-classes
conserved_regionc
part_ofop some telomerec

X_element_combinatorial_repeatc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001484

X element combinatorial repeats contain Tbf1p binding sites, and possible functions include a role in telomerase-independent telomere maintenance via recombination or as a barrier against transcriptional silencing. These are usually present as a combination of one or more of several types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
has super-classes
repeat_regionc
part_ofop some telomerec

X_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002030

has super-classes
mating_type_region_motifc

Y_prime_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001485

This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
has super-classes
repeat_regionc
part_ofop some telomerec

Y_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002001

Requested by Janos Demeter, SGD.
has super-classes
mating_type_region_motifc

Y_RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000405

has super-classes
ncRNAc

Y_RNA_primary_transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002042

has super-classes
nc_primary_transcriptc
has sub-classes
miR_encoding_Y_RNA_primary_transcriptc

YACc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000152

This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
vector_repliconc

YAC_clonec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000760

YAC_endc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001498

has super-classes
readc
part_ofop some YACc

YR_retrotransposonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002286

Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
has super-classes
non_LTR_retrotransposonc
has sub-classes
DIRS_YR_retrotransposonc, Ngaro_YR_retrotransposonc, Viper_YR_retrotransposonc

Z1_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002002

Requested by Janos Demeter, SGD.
has super-classes
mating_type_region_motifc

Z2_regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002003

Requested by Janos Demeter, SGD.
has super-classes
mating_type_region_motifc

Zas1_recognition_motifc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002215

has super-classes
DNA_motifc

zinc_finger_binding_sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001971

has super-classes
DNA_binding_sitec

zinc_repressed_elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0002006

This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe.
has super-classes
promoter_elementc
has sub-classes
LOZ1_response_elementc

Object Properties

adjacent_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#adjacent_to

associated_withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#associated_with

This relationship is vague and up for discussion.

complete_evidence_for_featureop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#complete_evidence_for_feature

If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

has characteristics: transitive

has super-properties
evidence_for_featureop

connects_onop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#connects_on

Example: A splice_junction connects_on exon, exon, mature_transcript.

contained_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#contained_by

The inverse is contains. Example: intein contained_by immature_peptide_region.

containsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#contains

Example: pre_miRNA contains miRNA_loop.

derives_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#derives_from

disconnected_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#disconnected_from

edited_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#edited_from

edited_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#edited_to

evidence_for_featureop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#evidence_for_feature

This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

has characteristics: transitive

has sub-properties
complete_evidence_for_featureop, partial_evidence_for_featureop

exemplar_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#exemplar_of

Tracker id: 2594157.

finished_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#finished_by

Example CDS finished_by stop_codon.

finishesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#finishes

Example: stop_codon finishes CDS.

gainedop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#gained

A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may gain a stop codon not present in the reference sequence.

genome_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#genome_of

guided_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#guided_by

guidesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#guides

has_integral_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#has_integral_part

Example: mRNA has_integral_part CDS.
has super-properties
has_partop

has_originop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#has_origin

has_partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#has_part

Example: operon has_part gene.
has sub-properties
has_integral_partop

has_qualityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#has_quality

The relationship between a feature and an attribute.

homologous_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#homologous_to

has characteristics: symmetric

has super-properties
similar_toop
has sub-properties
non_functional_homolog_ofop, orthologous_toop, paralogous_toop

integral_part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#integral_part_of

Example: exon integral_part_of transcript.
has super-properties
part_ofop

is_consecutive_sequence_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of

Example: region is consecutive_sequence of base.

lostop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#lost

A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may have lost a stop codon present in the reference sequence.

maximally_overlapsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#maximally_overlaps

Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.

member_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#member_of

A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.

has characteristics: transitive

has super-properties
part_ofop

non_functional_homolog_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#non_functional_homolog_of

has super-properties
homologous_toop

orthologous_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#orthologous_to

has characteristics: symmetric

has super-properties
homologous_toop

overlapsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#overlaps

Example: coding_exon overlaps CDS.

paralogous_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#paralogous_to

has characteristics: symmetric

has super-properties
homologous_toop

part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#part_of

Example: amino_acid part_of polypeptide.

has characteristics: transitive

has sub-properties
integral_part_ofop, member_ofop

partial_evidence_for_featureop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#partial_evidence_for_feature

has super-properties
evidence_for_featureop

position_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#position_of

processed_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#processed_from

Example: miRNA processed_from miRNA_primary_transcript.

processed_intoop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#processed_into

Example: miRNA_primary_transcript processed into miRNA.

recombined_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#recombined_from

recombined_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#recombined_to

sequence_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#sequence_of

similar_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#similar_to

has characteristics: symmetric

has sub-properties
homologous_toop

started_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#started_by

Example: CDS started_by start_codon.

startsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#starts

Example: start_codon starts CDS.

trans_spliced_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#trans_spliced_from

trans_spliced_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#trans_spliced_to

transcribed_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#transcribed_from

Example: primary_transcript transcribed_from gene.

transcribed_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#transcribed_to

Example: gene transcribed_to primary_transcript.

translates_toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#translates_to

Example: codon translates_to amino_acid.

translation_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#translation_of

Example: Polypeptide translation_of CDS.

variant_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/so#variant_of

Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.

Annotation Properties

Alliance of Genome Resourcesap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#AGR

has super-properties
synonym_type_propertyap

alliance of genome resourcesap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources

Alliance of Genome Resources Gene Biotype Slim
has super-properties
subset_propertyap

amino acid 1 letter codeap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#aa1

has super-properties
synonym_type_propertyap

amino acid 3 letter codeap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#aa3

has super-properties
synonym_type_propertyap

amino acid modificationap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#AAMOD

has super-properties
synonym_type_propertyap

auto generated byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#auto-generated-by

biosapiensap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#BS

has super-properties
synonym_type_propertyap

biosapiensap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#biosapiens

biosapiens protein feature ontology
has super-properties
subset_propertyap

commentap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2000/01/rdf-schema#comment

considerap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#consider

created byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#created_by

creation dateap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#creation_date

d b v a rap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#DBVAR

database of genomic structural variation
has super-properties
subset_propertyap

database_cross_referenceap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDbXref

dateap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#date

dbsnp variant termsap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#dbsnp

has super-properties
synonym_type_propertyap

DBVARap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#dbvar

has super-properties
synonym_type_propertyap

default namespaceap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#default-namespace

definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000115

deprecatedap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#deprecated

ensembl variant termsap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#ebi_variants

has super-properties
synonym_type_propertyap

has_alternative_idap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasAlternativeId

has_broad_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

has_exact_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

has_narrow_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym

has_obo_format_versionap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion

has_obo_namespaceap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasOBONamespace

has_related_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym

has_scopeap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasScope

has_synonym_typeap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasSynonymType

i a o 0000231ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000231

idap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#id

in_subsetap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#inSubset

labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2000/01/rdf-schema#label

RNA modificationap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#RNAMOD

has super-properties
synonym_type_propertyap

s o f aap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#SOFA

SO feature annotation
has super-properties
subset_propertyap

saved byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#saved-by

subset_propertyap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#SubsetProperty

has sub-properties
alliance of genome resourcesap, biosapiensap, d b v a rap, s o f aap

synonym_type_propertyap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty

has sub-properties
Alliance of Genome Resourcesap, DBVARap, RNA modificationap, amino acid 1 letter codeap, amino acid 3 letter codeap, amino acid modificationap, biosapiensap, dbsnp variant termsap, ensembl variant termsap, variant annotation termap

term replaced byap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0100001

variant annotation termap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/so#VAR

has super-properties
synonym_type_propertyap

Namespace Declarations back to ToC

default namespace
http://purl.obolibrary.org/obo/so.owl#
2021-07-12
http://purl.obolibrary.org/obo/so/2021-07-12/
obo
http://purl.obolibrary.org/obo/
oboInOwl
http://www.geneontology.org/formats/oboInOwl#
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
so
http://purl.obolibrary.org/obo/so#
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.